{"id":"https://openalex.org/W2770339797","doi":"https://doi.org/10.1109/tcbb.2017.2777448","title":"Protein-Protein Interaction Identification Using a Similarity-Constrained Graph Model","display_name":"Protein-Protein Interaction Identification Using a Similarity-Constrained Graph Model","publication_year":2017,"publication_date":"2017-11-24","ids":{"openalex":"https://openalex.org/W2770339797","doi":"https://doi.org/10.1109/tcbb.2017.2777448","mag":"2770339797","pmid":"https://pubmed.ncbi.nlm.nih.gov/29989990"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2017.2777448","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2017.2777448","pdf_url":null,"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":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":"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/A5100770856","display_name":"Yun Niu","orcid":"https://orcid.org/0000-0002-6841-3659"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Niu","raw_affiliation_strings":["College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Qinhuaiqu, Nanjing, Jiangsu, China"],"raw_orcid":"https://orcid.org/0000-0002-6841-3659","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Qinhuaiqu, Nanjing, Jiangsu, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034938775","display_name":"Hongmei Wu","orcid":"https://orcid.org/0000-0002-4974-0785"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongmei Wu","raw_affiliation_strings":["College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Qinhuaiqu, Nanjing, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Qinhuaiqu, Nanjing, Jiangsu, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100402317","display_name":"Yuwei Wang","orcid":"https://orcid.org/0000-0001-5782-1107"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuwei Wang","raw_affiliation_strings":["College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Qinhuaiqu, Nanjing, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Qinhuaiqu, Nanjing, Jiangsu, China","institution_ids":["https://openalex.org/I9842412"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.13607124,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"2","first_page":"607","last_page":"616"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962999820709229,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962999820709229,"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":0.9954000115394592,"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":0.994700014591217,"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":0.720790684223175},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6701406240463257},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5772561430931091},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5751371383666992},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5748460292816162},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5460696816444397},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5119534730911255},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5097774863243103},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49996161460876465},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4753192067146301},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46859613060951233},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.4614056646823883},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4432838559150696},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4192643165588379},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1301727592945099},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.074439138174057}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.720790684223175},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6701406240463257},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5772561430931091},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5751371383666992},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5748460292816162},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5460696816444397},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5119534730911255},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5097774863243103},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49996161460876465},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4753192067146301},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46859613060951233},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.4614056646823883},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4432838559150696},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4192643165588379},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1301727592945099},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.074439138174057},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2017.2777448","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2017.2777448","pdf_url":null,"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":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":"journal-article"},{"id":"pmid:29989990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29989990","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":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1169297611","display_name":null,"funder_award_id":"#61202132","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W137105571","https://openalex.org/W1493270114","https://openalex.org/W1567365482","https://openalex.org/W1968920591","https://openalex.org/W1969114498","https://openalex.org/W1976324729","https://openalex.org/W1986704581","https://openalex.org/W1993742718","https://openalex.org/W2025524803","https://openalex.org/W2064030835","https://openalex.org/W2085577304","https://openalex.org/W2098551466","https://openalex.org/W2098910027","https://openalex.org/W2100751507","https://openalex.org/W2103129421","https://openalex.org/W2103397879","https://openalex.org/W2108010925","https://openalex.org/W2109188334","https://openalex.org/W2109830295","https://openalex.org/W2122863289","https://openalex.org/W2127080518","https://openalex.org/W2128165179","https://openalex.org/W2130687290","https://openalex.org/W2133601033","https://openalex.org/W2135455794","https://openalex.org/W2144208076","https://openalex.org/W2146882220","https://openalex.org/W2148004186","https://openalex.org/W2157628440","https://openalex.org/W2163980860","https://openalex.org/W2164037733","https://openalex.org/W2166474856","https://openalex.org/W2166776180","https://openalex.org/W2171623083","https://openalex.org/W2468365289","https://openalex.org/W2915975108","https://openalex.org/W2946046356","https://openalex.org/W3147442204","https://openalex.org/W4255855797","https://openalex.org/W6605596884","https://openalex.org/W6629460809","https://openalex.org/W6667202976","https://openalex.org/W6678813022","https://openalex.org/W6681834304","https://openalex.org/W6684177858"],"related_works":["https://openalex.org/W1607472309","https://openalex.org/W4205958290","https://openalex.org/W2099369243","https://openalex.org/W4223656335","https://openalex.org/W2345184372","https://openalex.org/W2187500075","https://openalex.org/W2041399278","https://openalex.org/W2141705618","https://openalex.org/W2136184105","https://openalex.org/W3194539120"],"abstract_inverted_index":{"Protein-protein":[0],"interaction":[1],"(PPI)":[2],"identification":[3,143],"is":[4,78,86],"an":[5],"important":[6],"task":[7,40],"in":[8,63,88],"text":[9],"mining.":[10],"Most":[11],"PPI":[12,38,142],"detection":[13,39],"systems":[14],"make":[15,69],"predictions":[16],"solely":[17],"based":[18],"on":[19],"evidence":[20,81],"within":[21],"a":[22,42,54],"single":[23],"sentence":[24],"and":[25,57],"often":[26],"suffer":[27],"from":[28,41,53,82],"the":[29,47,64,83,89,99,114,135],"heavy":[30],"burden":[31],"of":[32,49,91],"manual":[33],"annotation.":[34],"This":[35],"paper":[36],"approaches":[37],"different":[43],"paradigm":[44],"by":[45],"investigating":[46],"context":[48,65],"protein":[50,76],"pairs":[51,77],"collected":[52],"large":[55],"corpus":[56],"their":[58],"relations.":[59],"First,":[60],"crucial":[61],"cues":[62],"are":[66],"exploited":[67],"to":[68],"initial":[70],"predictions.":[71],"Then,":[72],"relational":[73],"similarity":[74],"between":[75],"calculated.":[79],"Finally,":[80],"two":[84],"views":[85],"integrated":[87],"framework":[90],"minimum":[92],"cuts":[93],"algorithm.":[94],"Experimental":[95],"results":[96],"show":[97],"that":[98],"graph":[100],"model":[101],"achieves":[102,119],"better":[103],"performance":[104],"than":[105,122],"standard":[106],"supervised":[107],"approaches.":[108],"Using":[109],"20":[110],"percent":[111,129],"data":[112,130],"as":[113,131],"training":[115,132],"set,":[116],"our":[117],"algorithm":[118],"higher":[120],"accuracy":[121],"support":[123],"vector":[124],"machine":[125],"(SVM)":[126],"using":[127],"80":[128],"data.":[133,146],"Moreover,":[134],"semi-supervised":[136],"settings":[137],"reveal":[138],"promising":[139],"directions":[140],"for":[141],"exploiting":[144],"unlabeled":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}