{"id":"https://openalex.org/W4404413805","doi":"https://doi.org/10.1145/3703920","title":"Evolving to Find Optimizations Humans Miss: Using Evolutionary Computation to Improve GPU Code for Bioinformatics Applications","display_name":"Evolving to Find Optimizations Humans Miss: Using Evolutionary Computation to Improve GPU Code for Bioinformatics Applications","publication_year":2024,"publication_date":"2024-11-15","ids":{"openalex":"https://openalex.org/W4404413805","doi":"https://doi.org/10.1145/3703920"},"language":"en","primary_location":{"id":"doi:10.1145/3703920","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3703920","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3703920","source":{"id":"https://openalex.org/S4210221532","display_name":"ACM Transactions on Evolutionary Learning and Optimization","issn_l":"2688-299X","issn":["2688-299X","2688-3007"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Evolutionary Learning and Optimization","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3703920","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045603380","display_name":"Jhe-Yu Liou","orcid":"https://orcid.org/0000-0002-2497-7997"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jhe-Yu Liou","raw_affiliation_strings":["Arizona State University, Tempe, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0002-2497-7997","affiliations":[{"raw_affiliation_string":"Arizona State University, Tempe, AZ, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074495772","display_name":"Muaaz Gul Awan","orcid":"https://orcid.org/0000-0003-1233-1862"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Muaaz Awan","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-1233-1862","affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023632037","display_name":"Kirtus G. Leyba","orcid":"https://orcid.org/0000-0002-2360-8700"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirtus Leyba","raw_affiliation_strings":["Arizona State University, Tempe, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0002-2360-8700","affiliations":[{"raw_affiliation_string":"Arizona State University, Tempe, AZ, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047645496","display_name":"Petr \u0160ulc","orcid":"https://orcid.org/0000-0003-1565-6769"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Petr \u0160ulc","raw_affiliation_strings":["Arizona State University, Tempe, AZ, USA"],"raw_orcid":"https://orcid.org/0000-0003-1565-6769","affiliations":[{"raw_affiliation_string":"Arizona State University, Tempe, AZ, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016671058","display_name":"Steven Hofmeyr","orcid":"https://orcid.org/0000-0002-3299-472X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Hofmeyr","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-3299-472X","affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, CA, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028220093","display_name":"Carole-Jean Wu","orcid":"https://orcid.org/0000-0002-9032-7239"},"institutions":[{"id":"https://openalex.org/I4210099336","display_name":"Menlo School","ror":"https://ror.org/01240pn49","country_code":"US","type":"education","lineage":["https://openalex.org/I4210099336"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carole-Jean Wu","raw_affiliation_strings":["META, Menlo Park, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-9032-7239","affiliations":[{"raw_affiliation_string":"META, Menlo Park, CA, USA","institution_ids":["https://openalex.org/I4210099336"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114376382","display_name":"Stephanie Forrest","orcid":"https://orcid.org/0000-0002-5904-1646"},"institutions":[{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]},{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephanie Forrest","raw_affiliation_strings":["Arizona State University, Tempe, AZ, USA","Arizona State University, USA and Santa Fe Institute, USA"],"raw_orcid":"https://orcid.org/0000-0002-5904-1646","affiliations":[{"raw_affiliation_string":"Arizona State University, Tempe, AZ, USA","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"Arizona State University, USA and Santa Fe Institute, USA","institution_ids":["https://openalex.org/I1308548392","https://openalex.org/I55732556"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5045603380"],"corresponding_institution_ids":["https://openalex.org/I55732556"],"apc_list":null,"apc_paid":null,"fwci":0.8902,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.78637963,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"4","issue":"4","first_page":"1","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9851999878883362,"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":0.7250043153762817},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6077982187271118},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5539577603340149},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.552952766418457},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.4881506562232971},{"id":"https://openalex.org/keywords/evolutionary-computation","display_name":"Evolutionary computation","score":0.45345330238342285},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4161532521247864},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37480679154396057},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2575848400592804},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20763081312179565},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1780877709388733}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7250043153762817},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6077982187271118},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5539577603340149},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.552952766418457},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.4881506562232971},{"id":"https://openalex.org/C105902424","wikidata":"https://www.wikidata.org/wiki/Q1197129","display_name":"Evolutionary computation","level":2,"score":0.45345330238342285},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4161532521247864},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37480679154396057},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2575848400592804},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20763081312179565},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1780877709388733},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3703920","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3703920","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3703920","source":{"id":"https://openalex.org/S4210221532","display_name":"ACM Transactions on Evolutionary Learning and Optimization","issn_l":"2688-299X","issn":["2688-299X","2688-3007"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Evolutionary Learning and Optimization","raw_type":"journal-article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt2np4m99f","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/2np4m99f","pdf_url":"https://escholarship.org/content/qt2np4m99f/qt2np4m99f.pdf?t=smzhl2","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM Transactions on Evolutionary Learning and Optimization, vol 4, iss 4","raw_type":"article"},{"id":"pmh:ark:/13030/qt2np4m99f","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1145/3703920","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3703920","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3703920","source":{"id":"https://openalex.org/S4210221532","display_name":"ACM Transactions on Evolutionary Learning and Optimization","issn_l":"2688-299X","issn":["2688-299X","2688-3007"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Evolutionary Learning and Optimization","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2781752623","display_name":null,"funder_award_id":"DMR-2239518","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3557337367","display_name":null,"funder_award_id":"DMR-2239518","funder_id":"https://openalex.org/F4320337367","funder_display_name":"Division of Materials Research"},{"id":"https://openalex.org/G4895375649","display_name":null,"funder_award_id":"2211750","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4934994714","display_name":"CAREER: Design and modeling for modular bionanotechnology and citizen science","funder_award_id":"2239518","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6052857146","display_name":null,"funder_award_id":"N000142112876","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G7327021058","display_name":null,"funder_award_id":"2115075","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8473706846","display_name":null,"funder_award_id":"N000142012094","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320312777","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35"},{"id":"https://openalex.org/F4320332815","display_name":"Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"},{"id":"https://openalex.org/F4320337367","display_name":"Division of Materials Research","ror":"https://ror.org/01pc7k308"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4404413805.pdf"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W214093734","https://openalex.org/W1568631168","https://openalex.org/W1569348226","https://openalex.org/W1966343698","https://openalex.org/W1976203248","https://openalex.org/W1978397363","https://openalex.org/W1980199047","https://openalex.org/W1986396242","https://openalex.org/W1996761530","https://openalex.org/W2012436850","https://openalex.org/W2013779383","https://openalex.org/W2037748100","https://openalex.org/W2037963718","https://openalex.org/W2040010531","https://openalex.org/W2040492000","https://openalex.org/W2051039710","https://openalex.org/W2087064593","https://openalex.org/W2094878426","https://openalex.org/W2098232690","https://openalex.org/W2101153698","https://openalex.org/W2106683494","https://openalex.org/W2107824361","https://openalex.org/W2108556169","https://openalex.org/W2109405315","https://openalex.org/W2121344286","https://openalex.org/W2124677924","https://openalex.org/W2128120785","https://openalex.org/W2145373440","https://openalex.org/W2146899059","https://openalex.org/W2160145830","https://openalex.org/W2162960800","https://openalex.org/W2251236187","https://openalex.org/W2313116527","https://openalex.org/W2604766223","https://openalex.org/W2750779823","https://openalex.org/W2777654931","https://openalex.org/W2792271488","https://openalex.org/W2799953961","https://openalex.org/W2887327791","https://openalex.org/W2913348136","https://openalex.org/W2913954081","https://openalex.org/W2914237411","https://openalex.org/W2914304175","https://openalex.org/W2914697681","https://openalex.org/W2914826147","https://openalex.org/W2954767663","https://openalex.org/W2963909831","https://openalex.org/W3004705163","https://openalex.org/W3015537608","https://openalex.org/W3084730237","https://openalex.org/W3098605233","https://openalex.org/W3105247453","https://openalex.org/W3105350764","https://openalex.org/W3109066900","https://openalex.org/W3162291125","https://openalex.org/W3198685994","https://openalex.org/W4205232216","https://openalex.org/W4206218861","https://openalex.org/W4206625874","https://openalex.org/W4210368252","https://openalex.org/W4225342168","https://openalex.org/W4232270132","https://openalex.org/W4238128231","https://openalex.org/W4238306098","https://openalex.org/W4247885319","https://openalex.org/W4251637954","https://openalex.org/W4252074441","https://openalex.org/W4311263199","https://openalex.org/W4317666112","https://openalex.org/W4376272906"],"related_works":["https://openalex.org/W4399354997","https://openalex.org/W3062287","https://openalex.org/W2384867379","https://openalex.org/W2005148983","https://openalex.org/W2012954338","https://openalex.org/W2096672917","https://openalex.org/W2392023973","https://openalex.org/W1599154403","https://openalex.org/W1618681060","https://openalex.org/W2056396287"],"abstract_inverted_index":{"GPUs":[0,25],"are":[1,116,133],"used":[2],"in":[3],"many":[4,120],"settings":[5],"to":[6,21,28,61,150],"accelerate":[7],"large-scale":[8],"scientific":[9],"computation,":[10],"including":[11],"simulation,":[12],"computational":[13],"biology,":[14],"and":[15,37,43,78,85,118,160],"molecular":[16,79],"dynamics.":[17],"However,":[18],"optimizing":[19],"codes":[20],"run":[22],"efficiently":[23],"on":[24],"requires":[26],"developers":[27],"have":[29],"both":[30,151],"detailed":[31],"understanding":[32],"of":[33,40,69,94,102,114,121,145],"the":[34,67,95,103,111,122,130,143,153],"application":[35],"logic":[36],"significant":[38,108],"knowledge":[39],"parallel":[41],"programming":[42],"GPU":[44,52,126,139,165],"architectures.":[45,127],"This":[46],"paper":[47,89],"shows":[48],"that":[49,65,99],"an":[50,91],"automated":[51,146],"program":[53,147],"optimization":[54,148,154],"tool,":[55],"GEVO,":[56],"can":[57],"leverage":[58],"evolutionary":[59],"computation":[60],"find":[62],"code":[63],"edits":[64],"reduce":[66,152],"runtime":[68],"three":[70],"important":[71,105],"applications,":[72],"multiple":[73],"sequence":[74],"alignment,":[75],"agent-based":[76],"simulation":[77],"dynamics":[80],"codes,":[81],"by":[82],"28.9%,":[83],"29%,":[84],"17.8%":[86],"respectively.":[87],"The":[88],"presents":[90],"in-depth":[92],"analysis":[93],"discovered":[96,131],"optimizations,":[97],"revealing":[98],"(1)":[100],"several":[101],"most":[104],"optimizations":[106,123,132],"involve":[107],"epistasis,":[109],"(2)":[110],"primary":[112],"sources":[113],"improvement":[115],"application-specific,":[117],"(3)":[119],"generalize":[124],"across":[125],"In":[128],"general,":[129],"not":[134],"straightforward":[135],"even":[136],"for":[137,156,164],"a":[138],"human":[140,157],"expert,":[141],"showcasing":[142],"potential":[144],"tools":[149],"burden":[155],"domain":[158],"experts":[159],"provide":[161],"new":[162],"insights":[163],"experts.":[166]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
