{"id":"https://openalex.org/W4206505104","doi":"https://doi.org/10.1021/acs.jcim.1c00982","title":"Protein Interaction Network Reconstruction with a Structural Gated Attention Deep Model by Incorporating Network Structure Information","display_name":"Protein Interaction Network Reconstruction with a Structural Gated Attention Deep Model by Incorporating Network Structure Information","publication_year":2022,"publication_date":"2022-01-10","ids":{"openalex":"https://openalex.org/W4206505104","doi":"https://doi.org/10.1021/acs.jcim.1c00982","pmid":"https://pubmed.ncbi.nlm.nih.gov/35005980"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00982","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00982","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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":null,"display_name":"Fei Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Zhu","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University, Suzhou 215 006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou 215 006, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Feifei Li","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feifei Li","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University, Suzhou 215 006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou 215 006, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lei Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Deng","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University, Suzhou 215 006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University, Suzhou 215 006, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fanwang Meng","orcid":null},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Fanwang Meng","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada","institution_ids":["https://openalex.org/I98251732"]}]},{"author_position":"last","author":{"id":null,"display_name":"Zhongjie Liang","orcid":"https://orcid.org/0000-0003-0763-5407"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhongjie Liang","raw_affiliation_strings":["Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215 006, China"],"raw_orcid":"https://orcid.org/0000-0003-0763-5407","affiliations":[{"raw_affiliation_string":"Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215 006, China","institution_ids":["https://openalex.org/I3923682"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I3923682","https://openalex.org/I98251732"],"apc_list":null,"apc_paid":null,"fwci":0.6944,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65606275,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"62","issue":"2","first_page":"258","last_page":"273"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9164000153541565,"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":0.9164000153541565,"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":0.060100000351667404,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.002899999963119626,"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/robustness","display_name":"Robustness (evolution)","score":0.8349999785423279},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.560699999332428},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4320000112056732},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4296000003814697},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.41620001196861267},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.40139999985694885},{"id":"https://openalex.org/keywords/network-structure","display_name":"Network structure","score":0.3986999988555908},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.3610000014305115},{"id":"https://openalex.org/keywords/network-model","display_name":"Network model","score":0.3481999933719635}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.8349999785423279},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7764999866485596},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6671000123023987},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5855000019073486},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.560699999332428},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4320000112056732},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4296000003814697},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.41620001196861267},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.40139999985694885},{"id":"https://openalex.org/C2988224531","wikidata":"https://www.wikidata.org/wiki/Q20830730","display_name":"Network structure","level":2,"score":0.3986999988555908},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36480000615119934},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3610000014305115},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.3481999933719635},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3361999988555908},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.3345000147819519},{"id":"https://openalex.org/C2779136372","wikidata":"https://www.wikidata.org/wiki/Q10283002","display_name":"Information flow","level":2,"score":0.3271999955177307},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.32420000433921814},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3183000087738037},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3093000054359436},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.3052000105381012},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.28790000081062317},{"id":"https://openalex.org/C2993807640","wikidata":"https://www.wikidata.org/wiki/Q103709453","display_name":"Attention network","level":2,"score":0.2858999967575073},{"id":"https://openalex.org/C194544171","wikidata":"https://www.wikidata.org/wiki/Q21105679","display_name":"Gating","level":2,"score":0.28290000557899475},{"id":"https://openalex.org/C2779714256","wikidata":"https://www.wikidata.org/wiki/Q25305062","display_name":"Multiple Models","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2703000009059906},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.2660999894142151},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.2567000091075897},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.2517000138759613}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001288","descriptor_name":"Attention","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001288","descriptor_name":"Attention","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001288","descriptor_name":"Attention","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c00982","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00982","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:35005980","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35005980","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G21622510","display_name":null,"funder_award_id":"61303108","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G739385085","display_name":null,"funder_award_id":"BK20211102","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322769","display_name":"Natural Science Foundation of Jiangsu Province","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327518","display_name":"Priority Academic Program Development of Jiangsu Higher Education Institutions","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W76924599","https://openalex.org/W1518822923","https://openalex.org/W1888005072","https://openalex.org/W1963620624","https://openalex.org/W1965619419","https://openalex.org/W1982267716","https://openalex.org/W1985711767","https://openalex.org/W1993591356","https://openalex.org/W1995886170","https://openalex.org/W1999586982","https://openalex.org/W2001141328","https://openalex.org/W2009081245","https://openalex.org/W2018687970","https://openalex.org/W2043764521","https://openalex.org/W2044523575","https://openalex.org/W2072128103","https://openalex.org/W2075539007","https://openalex.org/W2077994671","https://openalex.org/W2097308346","https://openalex.org/W2097698606","https://openalex.org/W2106060578","https://openalex.org/W2108101947","https://openalex.org/W2117347512","https://openalex.org/W2119583098","https://openalex.org/W2132582966","https://openalex.org/W2143784594","https://openalex.org/W2150899372","https://openalex.org/W2152705149","https://openalex.org/W2155320925","https://openalex.org/W2155589321","https://openalex.org/W2156798505","https://openalex.org/W2160815625","https://openalex.org/W2165198854","https://openalex.org/W2165276227","https://openalex.org/W2169756968","https://openalex.org/W2170449776","https://openalex.org/W2284549295","https://openalex.org/W2341018731","https://openalex.org/W2393319904","https://openalex.org/W2493683088","https://openalex.org/W2517784737","https://openalex.org/W2603552761","https://openalex.org/W2604268533","https://openalex.org/W2616246685","https://openalex.org/W2616561032","https://openalex.org/W2620425337","https://openalex.org/W2735864034","https://openalex.org/W2789367970","https://openalex.org/W2795551885","https://openalex.org/W2801618929","https://openalex.org/W2804331675","https://openalex.org/W2810931990","https://openalex.org/W2885583144","https://openalex.org/W2886932769","https://openalex.org/W2890911678","https://openalex.org/W2898723593","https://openalex.org/W2900569176","https://openalex.org/W2901314256","https://openalex.org/W2901331306","https://openalex.org/W2950389803","https://openalex.org/W2972582951","https://openalex.org/W2977707586","https://openalex.org/W3004774000","https://openalex.org/W3007807538","https://openalex.org/W3021700383","https://openalex.org/W3022285953","https://openalex.org/W3023889133","https://openalex.org/W3042340477","https://openalex.org/W3087769169","https://openalex.org/W3089299640","https://openalex.org/W3100506610","https://openalex.org/W3116613266","https://openalex.org/W3136918052","https://openalex.org/W4288083766"],"related_works":[],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1],"(PPIs)":[2],"provide":[3],"a":[4,11,26,32,73,123,169,175],"physical":[5],"basis":[6],"of":[7,14,35,91,114,150,181],"molecular":[8],"communications":[9],"for":[10,31],"wide":[12],"range":[13],"biological":[15,36,183],"processes":[16],"in":[17,178],"living":[18],"cells.":[19],"Establishing":[20],"the":[21,58,78,89,108,115,147,157,179],"PPI":[22,92,116,182],"network":[23,93],"has":[24],"become":[25],"fundamental":[27],"but":[28],"essential":[29],"task":[30],"better":[33],"understanding":[34],"events":[37],"and":[38,67,111,138],"disease":[39],"pathogenesis.":[40],"Although":[41],"many":[42],"machine":[43],"learning":[44],"algorithms":[45],"have":[46],"been":[47],"employed":[48],"to":[49,87,126,130],"predict":[50],"PPIs,":[51],"with":[52,122],"only":[53],"protein":[54,105,166],"sequence":[55,106],"information":[56,112,164],"as":[57,174],"training":[59],"features,":[60],"these":[61],"models":[62],"suffer":[63],"from":[64],"low":[65],"robustness":[66,129],"prediction":[68],"accuracy.":[69],"In":[70],"this":[71],"study,":[72],"new":[74],"deep-learning-based":[75],"framework":[76],"named":[77],"Structural":[79],"Gated":[80],"Attention":[81],"Deep":[82],"(SGAD)":[83],"model":[84],"was":[85],"proposed":[86],"improve":[88,127],"performance":[90],"reconstruction":[94],"(PINR).":[95],"The":[96],"improved":[97],"predictive":[98],"performances":[99],"were":[100,119],"achieved":[101],"by":[102],"augmenting":[103],"multiple":[104],"descriptors,":[107],"topological":[109],"features":[110],"flow":[113],"network,":[117,172],"which":[118],"further":[120],"implemented":[121],"gating":[124],"mechanism":[125],"its":[128],"noise.":[131],"On":[132],"11":[133],"independent":[134],"test":[135],"data":[136,141],"sets":[137],"one":[139],"combined":[140],"set,":[142],"SGAD":[143,158],"yielded":[144],"area":[145],"under":[146],"curve":[148],"values":[149],"approximately":[151],"0.83-0.93,":[152],"outperforming":[153],"other":[154],"models.":[155],"Furthermore,":[156],"ensemble":[159],"can":[160],"learn":[161],"more":[162],"characteristics":[163],"on":[165],"pairs":[167],"through":[168],"two-layer":[170],"neural":[171],"serving":[173],"powerful":[176],"tool":[177],"exploration":[180],"space.":[184]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2022-01-26T00:00:00"}
