{"id":"https://openalex.org/W3137305549","doi":"https://doi.org/10.1109/tcbb.2021.3066591","title":"Hardware Acceleration of the STRIKE String Kernel Algorithm for Estimating Protein to Protein Interactions","display_name":"Hardware Acceleration of the STRIKE String Kernel Algorithm for Estimating Protein to Protein Interactions","publication_year":2021,"publication_date":"2021-03-17","ids":{"openalex":"https://openalex.org/W3137305549","doi":"https://doi.org/10.1109/tcbb.2021.3066591","mag":"3137305549","pmid":"https://pubmed.ncbi.nlm.nih.gov/33729945"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3066591","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3066591","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/9852343/09380998.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/9852343/09380998.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052845202","display_name":"Fadi N. Sibai","orcid":"https://orcid.org/0000-0002-9677-8911"},"institutions":[{"id":"https://openalex.org/I138564716","display_name":"Prince Mohammad bin Fahd University","ror":"https://ror.org/03d64na34","country_code":"SA","type":"education","lineage":["https://openalex.org/I138564716"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Fadi N. Sibai","raw_affiliation_strings":["College of Computer Engineering and Science, Prince Mohammad Bin Fahd University, Al-Khobar, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"College of Computer Engineering and Science, Prince Mohammad Bin Fahd University, Al-Khobar, Saudi Arabia","institution_ids":["https://openalex.org/I138564716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087689650","display_name":"Ali A. El\u2010Moursy","orcid":"https://orcid.org/0000-0002-3660-6544"},"institutions":[{"id":"https://openalex.org/I29891158","display_name":"University of Sharjah","ror":"https://ror.org/00engpz63","country_code":"AE","type":"education","lineage":["https://openalex.org/I29891158"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Ali El-Moursy","raw_affiliation_strings":["Computer Engineering Department, University of Sharjah, Sharjah, UAE"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, University of Sharjah, Sharjah, UAE","institution_ids":["https://openalex.org/I29891158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089499575","display_name":"Abu Asaduzzaman","orcid":"https://orcid.org/0000-0002-5041-1575"},"institutions":[{"id":"https://openalex.org/I39587148","display_name":"Wichita State University","ror":"https://ror.org/00c4e7y75","country_code":"US","type":"education","lineage":["https://openalex.org/I39587148"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abu Asaduzzaman","raw_affiliation_strings":["Electrical Engineering and Computer Science Department, Wichita State University, Wichita, KS, USA"],"affiliations":[{"raw_affiliation_string":"Electrical Engineering and Computer Science Department, Wichita State University, Wichita, KS, USA","institution_ids":["https://openalex.org/I39587148"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000482651","display_name":"Sohaib Majzoub","orcid":"https://orcid.org/0000-0003-3196-2635"},"institutions":[{"id":"https://openalex.org/I29891158","display_name":"University of Sharjah","ror":"https://ror.org/00engpz63","country_code":"AE","type":"education","lineage":["https://openalex.org/I29891158"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Sohaib Majzoub","raw_affiliation_strings":["Electrical Engineering Department, University of Sharjah, Sharjah, UAE"],"affiliations":[{"raw_affiliation_string":"Electrical Engineering Department, University of Sharjah, Sharjah, UAE","institution_ids":["https://openalex.org/I29891158"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5052845202"],"corresponding_institution_ids":["https://openalex.org/I138564716"],"apc_list":null,"apc_paid":null,"fwci":0.1609,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47161072,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"19","issue":"4","first_page":"2272","last_page":"2283"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9976000189781189,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9976000189781189,"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":0.9940999746322632,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9940000176429749,"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/verilog","display_name":"Verilog","score":0.7052680850028992},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.6920581459999084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6728416085243225},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6632777452468872},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.6336555480957031},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5756921768188477},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.532465934753418},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.5208902359008789},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4624069035053253},{"id":"https://openalex.org/keywords/execution-time","display_name":"Execution time","score":0.45704513788223267},{"id":"https://openalex.org/keywords/string-kernel","display_name":"String kernel","score":0.44838380813598633},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4187565743923187},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.21342679858207703},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.211836576461792},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15943175554275513},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1394844949245453}],"concepts":[{"id":"https://openalex.org/C2779030575","wikidata":"https://www.wikidata.org/wiki/Q827773","display_name":"Verilog","level":3,"score":0.7052680850028992},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.6920581459999084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6728416085243225},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6632777452468872},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.6336555480957031},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5756921768188477},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.532465934753418},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.5208902359008789},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4624069035053253},{"id":"https://openalex.org/C2989134064","wikidata":"https://www.wikidata.org/wiki/Q288510","display_name":"Execution time","level":2,"score":0.45704513788223267},{"id":"https://openalex.org/C55851704","wikidata":"https://www.wikidata.org/wiki/Q7623983","display_name":"String kernel","level":5,"score":0.44838380813598633},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4187565743923187},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.21342679858207703},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.211836576461792},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15943175554275513},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1394844949245453},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C160446489","wikidata":"https://www.wikidata.org/wiki/Q7226642","display_name":"Polynomial kernel","level":4,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000054","descriptor_name":"Acceleration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000054","descriptor_name":"Acceleration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000054","descriptor_name":"Acceleration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3066591","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3066591","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/9852343/09380998.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33729945","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33729945","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1109/tcbb.2021.3066591","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3066591","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/9852343/09380998.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320316805","display_name":"University of Sharjah","ror":"https://ror.org/00engpz63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3137305549.pdf","grobid_xml":"https://content.openalex.org/works/W3137305549.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W51518073","https://openalex.org/W164384110","https://openalex.org/W181072512","https://openalex.org/W1576213419","https://openalex.org/W1990315216","https://openalex.org/W1999556506","https://openalex.org/W2006899413","https://openalex.org/W2011427364","https://openalex.org/W2022180368","https://openalex.org/W2045131140","https://openalex.org/W2047606947","https://openalex.org/W2080922074","https://openalex.org/W2096041635","https://openalex.org/W2107425660","https://openalex.org/W2133540884","https://openalex.org/W2141885858","https://openalex.org/W2145427519","https://openalex.org/W2161701113","https://openalex.org/W2164328371","https://openalex.org/W2399715892","https://openalex.org/W2489967872","https://openalex.org/W2536158623","https://openalex.org/W2554813760","https://openalex.org/W2901683642","https://openalex.org/W4252166161","https://openalex.org/W4285719527","https://openalex.org/W6602022026","https://openalex.org/W6676236601"],"related_works":["https://openalex.org/W152351265","https://openalex.org/W2160069347","https://openalex.org/W3042295250","https://openalex.org/W2142835450","https://openalex.org/W4363649491","https://openalex.org/W2351404747","https://openalex.org/W3094476157","https://openalex.org/W2521029662","https://openalex.org/W2068282877","https://openalex.org/W2531676558"],"abstract_inverted_index":{"Protein-protein":[0],"interaction":[1],"(PPI)":[2],"is":[3,133],"an":[4],"important":[5],"field":[6],"in":[7,11,75],"bioinformatics":[8],"which":[9,37],"helps":[10],"understanding":[12],"diseases":[13],"and":[14,26,68,152,169],"devising":[15],"therapy.":[16],"PPI":[17,35,46,62],"aims":[18],"at":[19],"estimating":[20],"the":[21,69,91,97,108,117,120,129,155,178],"similarity":[22],"of":[23,58,72,119,142,163],"protein":[24,73,76],"sequences":[25,74,141],"their":[27],"common":[28],"regions.":[29],"STRIKE":[30,92,99,110,131,157],"was":[31,38],"introduced":[32],"as":[33],"a":[34,52,123],"algorithm":[36],"able":[39],"to":[40],"achieve":[41],"reasonable":[42],"improvement":[43,166],"over":[44,167],"existing":[45],"prediction":[47,63],"methods.":[48],"Although":[49],"it":[50],"consumes":[51],"lower":[53],"execution":[54,101,112],"time":[55,80],"than":[56,107],"most":[57],"other":[59],"state-of":[60],"the-art":[61],"methods,":[64],"its":[65],"compute-intensive":[66],"nature":[67],"large":[70],"volume":[71],"databases":[77],"necessitate":[78],"further":[79,115],"acceleration.":[81],"In":[82],"this":[83],"paper,":[84],"we":[85],"develop":[86],"hardware":[87],"accelerator":[88,100,111,126,159],"designs":[89],"for":[90,139],"algorithm.":[93],"Results":[94],"indicate":[95],"that":[96],"weighted":[98,121,130,156],"times":[102],"are":[103,175],"about":[104],"10x":[105],"longer":[106],"unweighted":[109],"times.":[113],"To":[114],"accelerate":[116],"performance":[118],"STRIKE,":[122],"parallel":[124,179],"module":[125,158,180],"organization":[127],"duplicating":[128],"modules":[132],"introduced,":[134],"achieving":[135],"near":[136],"linear":[137],"speedups":[138,174],"long":[140],"100":[143],"or":[144],"more":[145],"characters.":[146],"As":[147],"demonstrated":[148],"by":[149],"Verilog":[150],"simulations":[151],"FPGA":[153],"runs,":[154],"exhibits":[160],"three":[161],"orders":[162],"magnitude":[164],"speed":[165],"multi-core":[168],"cluster":[170],"computers.":[171],"Much":[172],"higher":[173],"possible":[176],"with":[177],"accelerator.":[181]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
