{"id":"https://openalex.org/W1553023756","doi":"https://doi.org/10.1186/s13637-016-0041-1","title":"Stochastic block coordinate Frank-Wolfe algorithm for large-scale biological network alignment","display_name":"Stochastic block coordinate Frank-Wolfe algorithm for large-scale biological network alignment","publication_year":2016,"publication_date":"2016-04-08","ids":{"openalex":"https://openalex.org/W1553023756","doi":"https://doi.org/10.1186/s13637-016-0041-1","mag":"1553023756","pmid":"https://pubmed.ncbi.nlm.nih.gov/27110234"},"language":"en","primary_location":{"id":"doi:10.1186/s13637-016-0041-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0041-1","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0041-1","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0041-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100429836","display_name":"Yijie Wang","orcid":"https://orcid.org/0000-0003-1656-8939"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yijie Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA","Department of Electrical and Computer Engineering, Texas A&M University,College Station,USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University,College Station,USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073946580","display_name":"Xiaoning Qian","orcid":"https://orcid.org/0000-0002-4347-2476"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoning Qian","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA","Department of Electrical and Computer Engineering, Texas A&M University,College Station,USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University, College Station, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Texas A&M University,College Station,USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100429836"],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":null,"apc_paid":null,"fwci":0.3486,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.67481235,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"2016","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9979000091552734,"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":0.7233707308769226},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.6169371604919434},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.5762781500816345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4929027557373047},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3742750883102417},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13379374146461487},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.10744109749794006},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.0732404887676239},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.07066264748573303}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7233707308769226},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.6169371604919434},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.5762781500816345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4929027557373047},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3742750883102417},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13379374146461487},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.10744109749794006},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0732404887676239},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.07066264748573303}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13637-016-0041-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0041-1","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0041-1","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},{"id":"pmid:27110234","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27110234","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":"EURASIP journal on bioinformatics & systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4826425","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4826425","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"EURASIP J Bioinform Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13637-016-0041-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0041-1","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0041-1","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1244356522","display_name":null,"funder_award_id":"1244068","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2419577208","display_name":null,"funder_award_id":"1447235","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3308757808","display_name":null,"funder_award_id":"R21DK092845","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G543285238","display_name":null,"funder_award_id":"#1447235","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7418893700","display_name":null,"funder_award_id":"R21DK092845","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1553023756.pdf","grobid_xml":"https://content.openalex.org/works/W1553023756.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1573602524","https://openalex.org/W1877183374","https://openalex.org/W2039950901","https://openalex.org/W2055666215","https://openalex.org/W2056124433","https://openalex.org/W2082366275","https://openalex.org/W2090963365","https://openalex.org/W2095984592","https://openalex.org/W2105864171","https://openalex.org/W2107427454","https://openalex.org/W2116117181","https://openalex.org/W2122961704","https://openalex.org/W2136885855","https://openalex.org/W2165253681","https://openalex.org/W2166574880","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"With":[0],"increasingly":[1],"\"big\"":[2],"data":[3,17,58],"available":[4],"in":[5,55,125],"biomedical":[6,57],"research,":[7],"deriving":[8],"accurate":[9],"and":[10,63,103,112],"reproducible":[11],"biology":[12],"knowledge":[13],"from":[14],"such":[15],"big":[16],"imposes":[18],"enormous":[19],"computational":[20,109],"challenges.":[21],"In":[22],"this":[23,132],"paper,":[24],"motivated":[25],"by":[26],"recently":[27],"developed":[28],"stochastic":[29,72,93],"block":[30,39,73,94],"coordinate":[31,40,74,95],"algorithms,":[32],"we":[33],"propose":[34],"a":[35],"highly":[36],"scalable":[37],"randomized":[38],"Frank-Wolfe":[41,96],"algorithm":[42,75,98],"for":[43,59,81,114,119,134],"convex":[44,49],"optimization":[45],"with":[46],"general":[47],"compact":[48],"constraints,":[50],"which":[51],"has":[52,99],"diverse":[53],"applications":[54],"analyzing":[56,135],"better":[60],"understanding":[61],"cellular":[62],"disease":[64],"mechanisms.":[65],"We":[66],"focus":[67],"on":[68,87],"implementing":[69],"the":[70,88,100,107,129],"derived":[71,92],"to":[76,106],"align":[77],"protein-protein":[78],"interaction":[79],"networks":[80,127],"identifying":[82],"conserved":[83,121],"functional":[84,122],"pathways":[85],"based":[86],"IsoRank":[89],"framework.":[90],"Our":[91,117],"(SBCFW)":[97],"convergence":[101],"guarantee":[102],"naturally":[104],"leads":[105],"decreased":[108],"cost":[110],"(time":[111],"space)":[113],"each":[115],"iteration.":[116],"experiments":[118],"querying":[120],"protein":[123],"complexes":[124],"yeast":[126],"confirm":[128],"effectiveness":[130],"of":[131],"technique":[133],"large-scale":[136],"biological":[137],"networks.":[138]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}