{"id":"https://openalex.org/W4408093238","doi":"https://doi.org/10.1016/j.future.2025.107786","title":"Cross-platform and polyhedral programming for Nussinov RNA folding","display_name":"Cross-platform and polyhedral programming for Nussinov RNA folding","publication_year":2025,"publication_date":"2025-03-04","ids":{"openalex":"https://openalex.org/W4408093238","doi":"https://doi.org/10.1016/j.future.2025.107786"},"language":"en","primary_location":{"id":"doi:10.1016/j.future.2025.107786","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.future.2025.107786","pdf_url":null,"source":{"id":"https://openalex.org/S186357190","display_name":"Future Generation Computer Systems","issn_l":"0167-739X","issn":["0167-739X","1872-7115"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Future Generation Computer Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1016/j.future.2025.107786","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078972354","display_name":"Mateusz Gru\u017cewski","orcid":"https://orcid.org/0000-0002-9419-2749"},"institutions":[{"id":"https://openalex.org/I155313962","display_name":"West Pomeranian University of Technology in Szczecin","ror":"https://ror.org/0596m7f19","country_code":"PL","type":"education","lineage":["https://openalex.org/I155313962"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mateusz Gruzewski","raw_affiliation_strings":["West Pomeranian University of Technology, Zolnierska 49, Szczecin, 71210, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"West Pomeranian University of Technology, Zolnierska 49, Szczecin, 71210, Poland","institution_ids":["https://openalex.org/I155313962"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044868188","display_name":"Marek Pa\u0142kowski","orcid":"https://orcid.org/0000-0002-5932-4523"},"institutions":[{"id":"https://openalex.org/I155313962","display_name":"West Pomeranian University of Technology in Szczecin","ror":"https://ror.org/0596m7f19","country_code":"PL","type":"education","lineage":["https://openalex.org/I155313962"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Marek Palkowski","raw_affiliation_strings":["West Pomeranian University of Technology, Zolnierska 49, Szczecin, 71210, Poland"],"raw_orcid":"https://orcid.org/0000-0002-5932-4523","affiliations":[{"raw_affiliation_string":"West Pomeranian University of Technology, Zolnierska 49, Szczecin, 71210, Poland","institution_ids":["https://openalex.org/I155313962"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044868188"],"corresponding_institution_ids":["https://openalex.org/I155313962"],"apc_list":{"value":3000,"currency":"USD","value_usd":3000},"apc_paid":{"value":3000,"currency":"USD","value_usd":3000},"fwci":1.918,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.84547396,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"169","issue":null,"first_page":"107786","last_page":"107786"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","score":0.9968000054359436,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.991599977016449,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.867321252822876},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4578898847103119},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32663673162460327}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.867321252822876},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4578898847103119},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32663673162460327},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1016/j.future.2025.107786","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.future.2025.107786","pdf_url":null,"source":{"id":"https://openalex.org/S186357190","display_name":"Future Generation Computer Systems","issn_l":"0167-739X","issn":["0167-739X","1872-7115"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Future Generation Computer Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1016/j.future.2025.107786","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.future.2025.107786","pdf_url":null,"source":{"id":"https://openalex.org/S186357190","display_name":"Future Generation Computer Systems","issn_l":"0167-739X","issn":["0167-739X","1872-7115"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Future Generation Computer Systems","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1491410022","https://openalex.org/W1503700136","https://openalex.org/W1675130169","https://openalex.org/W2015478888","https://openalex.org/W2050718845","https://openalex.org/W2054931730","https://openalex.org/W2077143534","https://openalex.org/W2087001748","https://openalex.org/W2087064593","https://openalex.org/W2102976251","https://openalex.org/W2132331020","https://openalex.org/W2141607439","https://openalex.org/W2498116915","https://openalex.org/W2621218774","https://openalex.org/W2774084933","https://openalex.org/W2774679324","https://openalex.org/W2990138404","https://openalex.org/W3151489216","https://openalex.org/W3203568064","https://openalex.org/W3204307791","https://openalex.org/W4231485196","https://openalex.org/W4248073216","https://openalex.org/W4249697788","https://openalex.org/W4252485723","https://openalex.org/W4281769137","https://openalex.org/W4299626558","https://openalex.org/W4307227773","https://openalex.org/W4321486842","https://openalex.org/W4391169057","https://openalex.org/W4409063370","https://openalex.org/W6632224712","https://openalex.org/W6634002253","https://openalex.org/W6666218771","https://openalex.org/W6676721328","https://openalex.org/W6678377514","https://openalex.org/W6679466897","https://openalex.org/W6680431041","https://openalex.org/W6749394860","https://openalex.org/W6778883912","https://openalex.org/W6783270390","https://openalex.org/W6800086383","https://openalex.org/W6860487596"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"This":[0],"article":[1],"addresses":[2],"the":[3,57,60,67,77,104,120,133,150,173,179,182,185,191],"use":[4,41],"of":[5,79,106,181,232],"codes":[6,139,201,227,234],"from":[7,149],"polyhedral":[8,164],"compilers":[9],"with":[10,157],"tiled":[11,219],"and":[12,51,59,103,169,218,222,235,244],"parallel":[13,217],"code":[14,80,165],"designed":[15,81],"for":[16,24,82,209],"CPU":[17,220],"processors,":[18],"automatically":[19,137],"generated":[20,138,224],"as":[21],"source-to-source":[22],"OpenMP":[23],"NVIDIA":[25,134,207],"GPU":[26,226],"graphics":[27],"cards":[28],"using":[29,184,228],"CUDA.":[30],"In":[31,115],"previous":[32],"publications,":[33],"we":[34,118],"demonstrated":[35],"that":[36,167],"it":[37],"is":[38,70,197],"possible":[39],"to":[40,46,86,111,128,216,241],"large":[42],"language":[43],"models":[44],"(LLM)":[45],"translate":[47],"code,":[48],"generate":[49],"kernels,":[50],"correctly":[52],"manage":[53],"memory":[54,194],"transfers":[55],"between":[56,96],"host":[58],"device":[61],"without":[62],"manual":[63],"effort.":[64],"Unfortunately,":[65],"when":[66,89],"target":[68],"architecture":[69],"not":[71],"taken":[72],"into":[73],"account":[74],"in":[75,126],"detail,":[76],"performance":[78,112,131],"CPUs":[83],"leaves":[84],"much":[85],"be":[87],"desired":[88],"running":[90],"on":[91,132,204],"GPUs.":[92],"The":[93,199,230],"architectural":[94],"differences":[95],"these":[97,233],"two":[98,205],"platforms":[99],"like":[100],"cores,":[101],"cache,":[102],"dimensionality":[105],"computations":[107],"require":[108],"careful":[109],"attention":[110],"portability":[113],".":[114],"this":[116],"article,":[117],"address":[119],"Nussinov":[121],"algorithm,":[122],"a":[123,146,163],"popular":[124],"benchmark":[125,156],"bioinformatics,":[127],"achieve":[129],"higher":[130],"platform":[135],"than":[136],"by":[140],"LLM.":[141],"Nussinov\u2019s":[142,225],"loop":[143,176],"nests":[144],"are":[145,247],"non-trivial":[147],"kernel":[148],"non-serial":[151],"polyadic":[152],"dynamic":[153],"programming":[154],"(NPDP)":[155],"non-uniform":[158],"loops.":[159],"We":[160],"will":[161],"utilize":[162],"framework":[166],"tiles":[168],"then":[170],"manually":[171],"modifies":[172],"most":[174],"nested":[175],"nest":[177],"containing":[178],"majority":[180],"computations,":[183,192],"two-dimensional":[186],"thread":[187],"blocks.":[188],"To":[189],"accelerate":[190],"shared":[193],"within":[195],"blocks":[196],"utilized.":[198],"resulting":[200],"were":[202,238],"tested":[203],"modern":[206],"devices":[208],"various":[210],"RNA":[211],"sequence":[212],"lengths":[213],",":[214],"compared":[215],"codes,":[221],"previously":[223],"LLMs.":[229],"correctness":[231],"their":[236],"scalability":[237],"analyzed.":[239],"Comparison":[240],"related":[242],"approaches":[243],"future":[245],"work":[246],"outlined.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}