{"id":"https://openalex.org/W2136940180","doi":"https://doi.org/10.1109/titb.2009.2028234","title":"Predicting Protein Function by Frequent Functional Association Pattern Mining in Protein Interaction Networks","display_name":"Predicting Protein Function by Frequent Functional Association Pattern Mining in Protein Interaction Networks","publication_year":2009,"publication_date":"2009-09-04","ids":{"openalex":"https://openalex.org/W2136940180","doi":"https://doi.org/10.1109/titb.2009.2028234","mag":"2136940180","pmid":"https://pubmed.ncbi.nlm.nih.gov/19726271"},"language":"en","primary_location":{"id":"doi:10.1109/titb.2009.2028234","is_oa":false,"landing_page_url":"https://doi.org/10.1109/titb.2009.2028234","pdf_url":null,"source":{"id":"https://openalex.org/S68937846","display_name":"IEEE Transactions on Information Technology in Biomedicine","issn_l":"1089-7771","issn":["1089-7771","1558-0032"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Information Technology in Biomedicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5013149893","display_name":"Young\u2010Rae Cho","orcid":"https://orcid.org/0000-0002-4645-2542"},"institutions":[{"id":"https://openalex.org/I157394403","display_name":"Baylor University","ror":"https://ror.org/005781934","country_code":"US","type":"education","lineage":["https://openalex.org/I157394403"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Young-Rae Cho","raw_affiliation_strings":["Department of Computer Science, Baylor University,Waco, TX 76798, USA. young-rae_cho@baylor.edu","Department of Computer Science Baylor University Waco TX USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Baylor University,Waco, TX 76798, USA. young-rae_cho@baylor.edu","institution_ids":["https://openalex.org/I157394403"]},{"raw_affiliation_string":"Department of Computer Science Baylor University Waco TX USA","institution_ids":["https://openalex.org/I157394403"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101490494","display_name":"Aidong Zhang","orcid":"https://orcid.org/0000-0002-7050-4648"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aidong Zhang","raw_affiliation_strings":["Department of Computer Science and Engineering, State University of New York, Buffalo, NY, USA","Department of Computer Science & Engineering, State University of New York, Buffalo, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Department of Computer Science & Engineering, State University of New York, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013149893"],"corresponding_institution_ids":["https://openalex.org/I157394403"],"apc_list":null,"apc_paid":null,"fwci":1.0784,"has_fulltext":false,"cited_by_count":59,"citation_normalized_percentile":{"value":0.76806189,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"14","issue":"1","first_page":"30","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9919000267982483,"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/T13127","display_name":"Biotin and Related Studies","score":0.9815000295639038,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/protein-interaction-networks","display_name":"Protein Interaction Networks","score":0.6263000965118408},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.6010978817939758},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5926028490066528},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.5884630680084229},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.5436647534370422},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.5150363445281982},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.49709847569465637},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.46310871839523315},{"id":"https://openalex.org/keywords/a-priori-and-a-posteriori","display_name":"A priori and a posteriori","score":0.4541834890842438},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.44936785101890564},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.42172810435295105},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4195246398448944},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.41225725412368774},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41079646348953247},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4022263288497925},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3671739101409912},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36166393756866455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2509208917617798},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22420719265937805},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12957611680030823},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12297207117080688}],"concepts":[{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.6263000965118408},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.6010978817939758},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5926028490066528},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5884630680084229},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.5436647534370422},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.5150363445281982},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.49709847569465637},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.46310871839523315},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.4541834890842438},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.44936785101890564},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.42172810435295105},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4195246398448944},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.41225725412368774},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41079646348953247},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4022263288497925},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3671739101409912},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36166393756866455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2509208917617798},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22420719265937805},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12957611680030823},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12297207117080688},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/titb.2009.2028234","is_oa":false,"landing_page_url":"https://doi.org/10.1109/titb.2009.2028234","pdf_url":null,"source":{"id":"https://openalex.org/S68937846","display_name":"IEEE Transactions on Information Technology in Biomedicine","issn_l":"1089-7771","issn":["1089-7771","1558-0032"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Information Technology in Biomedicine","raw_type":"journal-article"},{"id":"pmid:19726271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19726271","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 transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1486817521","https://openalex.org/W1506285740","https://openalex.org/W1995907191","https://openalex.org/W2011986160","https://openalex.org/W2026353653","https://openalex.org/W2042210880","https://openalex.org/W2066235893","https://openalex.org/W2072372949","https://openalex.org/W2090766471","https://openalex.org/W2107710781","https://openalex.org/W2118349699","https://openalex.org/W2118957335","https://openalex.org/W2123318061","https://openalex.org/W2124533460","https://openalex.org/W2130687290","https://openalex.org/W2141629057","https://openalex.org/W2153624566","https://openalex.org/W2161917555","https://openalex.org/W2168209541","https://openalex.org/W2171403830","https://openalex.org/W3039539181","https://openalex.org/W3199143553","https://openalex.org/W6780396083"],"related_works":["https://openalex.org/W2800059693","https://openalex.org/W1987705964","https://openalex.org/W2414873431","https://openalex.org/W2287132924","https://openalex.org/W2593939008","https://openalex.org/W2586268529","https://openalex.org/W2125650596","https://openalex.org/W1509891158","https://openalex.org/W2131407941","https://openalex.org/W2154613611"],"abstract_inverted_index":{"Predicting":[0],"protein":[1,4,70,79,147],"function":[2,21,59,161],"from":[3],"interaction":[5,71,148],"networks":[6],"has":[7,39,189],"been":[8,40],"challenging":[9],"because":[10],"of":[11,14,28,47,65,75,124,198,214,220],"the":[12,26,30,44,84,109,117,122,138,145,167,170,174,212],"complexity":[13],"functional":[15,45,66,91,110,157,203,218],"relationships":[16],"among":[17],"proteins.":[18,35,49],"Most":[19],"previous":[20,193],"prediction":[22,60,162,199],"methods":[23,195],"depend":[24],"on":[25],"neighborhood":[27],"or":[29],"connected":[31],"paths":[32],"to":[33,43,178],"known":[34],"However,":[36],"their":[37],"accuracy":[38],"limited":[41],"due":[42],"inconsistency":[46],"interacting":[48],"In":[50],"this":[51,208],"paper,":[52],"we":[53,184],"propose":[54],"a":[55,69,78,88,98,131,141,223],"novel":[56],"approach":[57,188],"for":[58,217],"by":[61,127,133,140,165],"identifying":[62],"frequent":[63,102,125,156,175,202],"patterns":[64,112,126,176,205],"associations":[67],"in":[68,116,196,207,222],"network.":[72,118],"A":[73,90],"set":[74],"functions":[76],"that":[77,113,186],"performs":[80],"is":[81,94,163],"assigned":[82],"into":[83],"corresponding":[85],"node":[86,129],"as":[87,97],"label.":[89],"association":[92,111,158,204],"pattern":[93],"then":[95],"represented":[96],"labeled":[99,103],"subgraph.":[100],"Our":[101],"subgraph":[104],"mining":[105],"algorithm":[106,151],"efficiently":[107],"searches":[108],"occur":[114],"frequently":[115],"It":[119],"iteratively":[120],"increases":[121],"size":[123],"one":[128],"at":[130],"time":[132],"selective":[134],"joining,":[135],"and":[136],"simplifies":[137],"network":[139],"priori":[142],"pruning.":[143],"Using":[144],"yeast":[146],"network,":[149],"our":[150,187],"found":[152],"more":[153],"than":[154,192],"1400":[155],"patterns.":[159],"The":[160,201],"performed":[164],"matching":[166],"subgraph,":[168],"including":[169],"unknown":[171],"protein,":[172],"with":[173],"analogous":[177],"it.":[179],"By":[180],"leave-one-out":[181],"cross":[182],"validation,":[183],"show":[185],"better":[190],"performance":[191],"link-based":[194],"terms":[197],"accuracy.":[200],"generated":[206],"study":[209],"might":[210],"become":[211],"foundations":[213],"advanced":[215],"analysis":[216],"behaviors":[219],"proteins":[221],"system":[224],"level.":[225]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
