{"id":"https://openalex.org/W4212863848","doi":"https://doi.org/10.1145/3503222.3507722","title":"ProSE: the architecture and design of a protein discovery engine","display_name":"ProSE: the architecture and design of a protein discovery engine","publication_year":2022,"publication_date":"2022-02-22","ids":{"openalex":"https://openalex.org/W4212863848","doi":"https://doi.org/10.1145/3503222.3507722"},"language":"en","primary_location":{"id":"doi:10.1145/3503222.3507722","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3503222.3507722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008887305","display_name":"Eyes S Robson","orcid":"https://orcid.org/0000-0001-7159-0974"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eyes Robson","raw_affiliation_strings":["University of California at Berkeley, USA"],"affiliations":[{"raw_affiliation_string":"University of California at Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036627994","display_name":"Ceyu Xu","orcid":"https://orcid.org/0000-0002-2668-6456"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ceyu Xu","raw_affiliation_strings":["Duke University, USA"],"affiliations":[{"raw_affiliation_string":"Duke University, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042221799","display_name":"Lisa Wu Wills","orcid":"https://orcid.org/0000-0002-3574-3440"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lisa Wu Wills","raw_affiliation_strings":["Duke University, USA"],"affiliations":[{"raw_affiliation_string":"Duke University, USA","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008887305"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":0.6862,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65421918,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"655","last_page":"668"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9987000226974487,"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":0.9947999715805054,"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/speedup","display_name":"Speedup","score":0.9127814173698425},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7551987171173096},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.6275070309638977},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5979309678077698},{"id":"https://openalex.org/keywords/microarchitecture","display_name":"Microarchitecture","score":0.5185602307319641},{"id":"https://openalex.org/keywords/generality","display_name":"Generality","score":0.4755796492099762},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4673123061656952},{"id":"https://openalex.org/keywords/inference-engine","display_name":"Inference engine","score":0.44896554946899414},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.429055780172348},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.42127370834350586},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.41293424367904663},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4057241976261139},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17624062299728394}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.9127814173698425},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7551987171173096},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.6275070309638977},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5979309678077698},{"id":"https://openalex.org/C107598950","wikidata":"https://www.wikidata.org/wiki/Q259864","display_name":"Microarchitecture","level":2,"score":0.5185602307319641},{"id":"https://openalex.org/C2780767217","wikidata":"https://www.wikidata.org/wiki/Q5532421","display_name":"Generality","level":2,"score":0.4755796492099762},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4673123061656952},{"id":"https://openalex.org/C46743427","wikidata":"https://www.wikidata.org/wiki/Q1341685","display_name":"Inference engine","level":3,"score":0.44896554946899414},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.429055780172348},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.42127370834350586},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.41293424367904663},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4057241976261139},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17624062299728394},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3503222.3507722","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3503222.3507722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.6899999976158142,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W2041770021","https://openalex.org/W2054095206","https://openalex.org/W2283896596","https://openalex.org/W2537959404","https://openalex.org/W2588191434","https://openalex.org/W2605347906","https://openalex.org/W2606722458","https://openalex.org/W2612387305","https://openalex.org/W2625457103","https://openalex.org/W2900228909","https://openalex.org/W2906043559","https://openalex.org/W2944853256","https://openalex.org/W2945146780","https://openalex.org/W2951122824","https://openalex.org/W2953292182","https://openalex.org/W2956569764","https://openalex.org/W2972054167","https://openalex.org/W2980200167","https://openalex.org/W2980789587","https://openalex.org/W2981849318","https://openalex.org/W2995472818","https://openalex.org/W3002639525","https://openalex.org/W3016542674","https://openalex.org/W3028661980","https://openalex.org/W3036878841","https://openalex.org/W3099513244","https://openalex.org/W3101026687","https://openalex.org/W3146944767","https://openalex.org/W3177828909","https://openalex.org/W3179485843","https://openalex.org/W3189877953","https://openalex.org/W3191761521","https://openalex.org/W3211728297","https://openalex.org/W4244024631"],"related_works":["https://openalex.org/W2045049461","https://openalex.org/W1978893398","https://openalex.org/W2201908702","https://openalex.org/W4381094582","https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2369625323","https://openalex.org/W2364579609","https://openalex.org/W1977906818","https://openalex.org/W2099629705"],"abstract_inverted_index":{"Protein":[0,108],"language":[1],"models":[2,26],"have":[3],"enabled":[4],"breakthrough":[5],"approaches":[6],"to":[7,19,100,113,122,130,141],"protein":[8,56],"structure":[9],"prediction,":[10],"function":[11],"annotation,":[12],"and":[13,36,51,58,74,116,135],"drug":[14],"discovery.":[15],"A":[16],"primary":[17],"limitation":[18],"the":[20,28,34,48],"widespread":[21],"adoption":[22],"of":[23,38,54,69],"these":[24,39],"powerful":[25],"is":[27],"high":[29],"computational":[30],"cost":[31],"associated":[32],"with":[33,89],"training":[35],"inference":[37,110],"models,":[40],"especially":[41],"at":[42,111],"longer":[43],"sequence":[44],"lengths.":[45],"We":[46],"present":[47],"architecture,":[49],"microarchitecture,":[50],"hardware":[52],"implementation":[53],"a":[55,67],"design":[57],"discovery":[59],"accelerator,":[60],"ProSE":[61,65,106,127],"(Protein":[62],"Systolic":[63],"Engine).":[64],"has":[66],"collection":[68],"custom":[70],"heterogeneous":[71],"systolic":[72,90],"arrays":[73],"special":[75],"functions":[76],"that":[77],"process":[78],"transfer":[79],"learning":[80],"model":[81,98],"inferences":[82],"efficiently.":[83],"The":[84],"architecture":[85],"marries":[86],"SIMD-style":[87],"computations":[88],"array":[91],"architectures,":[92],"optimizing":[93],"coarse-grained":[94],"operation":[95],"sequences":[96],"across":[97],"layers":[99],"achieve":[101],"efficiency":[102,119,139],"without":[103],"sacrificing":[104],"generality.":[105],"performs":[107],"BERT":[109],"up":[112,129],"6.9\u00d7":[114],"speedup":[115,134],"48\u00d7":[117],"power":[118,138],"(performance/Watt)":[120],"compared":[121,140],"one":[123],"NVIDIA":[124],"A100":[125],"GPU.":[126],"achieves":[128],"5.5":[131],"\u00d7":[132],"(12.7\u00d7)":[133],"173\u00d7":[136],"(249\u00d7)":[137],"TPUv3":[142],"(TPUv2).":[143]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
