{"id":"https://openalex.org/W4416946926","doi":"https://doi.org/10.1109/tcbbio.2025.3638901","title":"Spatial Hierarchical Protein-Protein Interaction Site Prediction Using Squeeze-and-Excitation Capsule Networks","display_name":"Spatial Hierarchical Protein-Protein Interaction Site Prediction Using Squeeze-and-Excitation Capsule Networks","publication_year":2025,"publication_date":"2025-12-01","ids":{"openalex":"https://openalex.org/W4416946926","doi":"https://doi.org/10.1109/tcbbio.2025.3638901","pmid":"https://pubmed.ncbi.nlm.nih.gov/41325125"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3638901","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3638901","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE 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/A5045837259","display_name":"Weipeng Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weipeng Lv","raw_affiliation_strings":["College of Computer Science and Software Engineering and the National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-6669-6595","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering and the National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Changkun Jiang","orcid":"https://orcid.org/0000-0003-2772-2348"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changkun Jiang","raw_affiliation_strings":["College of Computer Science and Software Engineering and the National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0003-2772-2348","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering and the National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100393871","display_name":"Jianqiang Li","orcid":"https://orcid.org/0000-0002-2208-962X"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianqiang Li","raw_affiliation_strings":["College of Computer Science and Software Engineering and the National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-2208-962X","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering and the National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28435322,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"1","first_page":"163","last_page":"175"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8080000281333923,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.8080000281333923,"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":0.11819999665021896,"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":0.03420000150799751,"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/representation","display_name":"Representation (politics)","score":0.6449000239372253},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.6115999817848206},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.49470001459121704},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.39309999346733093},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3767000138759613},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.36800000071525574},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.3409000039100647},{"id":"https://openalex.org/keywords/amino-acid-residue","display_name":"Amino acid residue","score":0.3190000057220459}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7059999704360962},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6449000239372253},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.6115999817848206},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.603600025177002},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.49470001459121704},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46399998664855957},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4196999967098236},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.39309999346733093},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3767000138759613},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.36800000071525574},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.3409000039100647},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.3190000057220459},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.3167000114917755},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3156000077724457},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.2939000129699707},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.28859999775886536},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.28760001063346863},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.2797999978065491},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.27090001106262207},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2671999931335449},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2628999948501587},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2587999999523163}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3638901","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3638901","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41325125","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41325125","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 computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3165776435","display_name":null,"funder_award_id":"2025A1515010278","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G4804518518","display_name":"\u6709\u9650\u7406\u6027\u4e0b\u7fa4\u667a\u611f\u77e5\u7684\u6fc0\u52b1\u673a\u5236\u7814\u7a76","funder_award_id":"61902255","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/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1815147785","https://openalex.org/W1990315216","https://openalex.org/W2004360551","https://openalex.org/W2009672036","https://openalex.org/W2010022403","https://openalex.org/W2029476353","https://openalex.org/W2057271915","https://openalex.org/W2057813163","https://openalex.org/W2073229442","https://openalex.org/W2087192353","https://openalex.org/W2094148990","https://openalex.org/W2103485392","https://openalex.org/W2109228802","https://openalex.org/W2127771490","https://openalex.org/W2130479394","https://openalex.org/W2141627824","https://openalex.org/W2142529984","https://openalex.org/W2152811165","https://openalex.org/W2155194485","https://openalex.org/W2158714788","https://openalex.org/W2162682281","https://openalex.org/W2280888683","https://openalex.org/W2511002675","https://openalex.org/W2570083522","https://openalex.org/W2722005050","https://openalex.org/W2752782242","https://openalex.org/W2891614933","https://openalex.org/W2917858269","https://openalex.org/W2944679105","https://openalex.org/W2950374603","https://openalex.org/W2971405760","https://openalex.org/W2984274952","https://openalex.org/W3080498684","https://openalex.org/W3197696221","https://openalex.org/W3212342036","https://openalex.org/W4206247924","https://openalex.org/W4221091806","https://openalex.org/W4308516830","https://openalex.org/W4313525379","https://openalex.org/W4362522229","https://openalex.org/W4386634093","https://openalex.org/W4403085080","https://openalex.org/W4404021861","https://openalex.org/W4414732532"],"related_works":[],"abstract_inverted_index":{"The":[0,116,183],"discovery":[1],"of":[2,13,51,82,119,132,151,173,205],"protein-protein":[3],"interaction":[4,92],"(PPI)":[5],"sites":[6,21,93],"is":[7,121,147],"vital":[8],"for":[9,25],"exploring":[10],"the":[11,48,64,80,126,130,137,160,181,190,201],"principles":[12],"PPIs.":[14],"Developing":[15],"computational":[16],"approaches":[17],"to":[18,42,62,86,89,108,122,158,169,179],"predict":[19,43],"PPI":[20,44,110],"can":[22],"effectively":[23,90],"compensate":[24],"biological":[26],"experiments,":[27],"which":[28,146],"are":[29],"mostly":[30],"time-consuming":[31],"and":[32,56,72,176,195,209],"vulnerable-to-noise.":[33],"In":[34,98],"recent":[35],"years,":[36],"deep":[37],"learning":[38],"has":[39],"been":[40],"used":[41],"sites,":[45],"by":[46,140],"considering":[47],"contextual":[49],"information":[50],"target":[52],"amino":[53],"acid":[54],"residues":[55],"using":[57],"a":[58,104,142,148],"local":[59],"protein":[60,83,133,174],"sequence":[61],"represent":[63],"targets.":[65],"However,":[66],"traditional":[67],"deep-learning":[68,106],"techniques,":[69],"e.g.,":[70],"DNNs":[71],"CNNs,":[73],"disregard":[74],"important":[75],"spatial":[76,114],"hierarchies":[77],"contained":[78],"in":[79,200],"features":[81,131,172],"sequences,":[84],"leading":[85],"their":[87],"failure":[88],"distinguish":[91],"from":[94],"different":[95],"residue":[96],"regions.":[97],"this":[99],"work,":[100],"we":[101],"design":[102],"MSE-CapsPPISP,":[103],"new":[105],"model":[107],"address":[109],"site":[111],"prediction":[112],"with":[113,154],"hierarchies.":[115],"key":[117,203],"idea":[118],"MSE-CapsPPISP":[120,165,188],"take":[123],"into":[124],"account":[125],"hierarchical":[127,138],"relationships":[128,139],"between":[129],"sequences.":[134],"We":[135],"characterize":[136],"designing":[141],"tailored":[143],"Capsule":[144],"Network,":[145],"novel":[149],"type":[150],"neural":[152],"network":[153,161],"vector":[155],"neurons.":[156],"Moreover,":[157],"make":[159],"representation":[162],"more":[163],"robust,":[164],"uses":[166],"multi-scale":[167,171],"CNNs":[168],"extract":[170],"sequences":[175],"Squeeze-and-Excitation":[177],"blocks":[178],"recalibrate":[180],"features.":[182],"validation":[184],"results":[185],"show":[186],"that":[187],"outperforms":[189],"baseline":[191],"CNNs-based":[192],"architecture":[193],"DeepPPISP":[194],"other":[196],"existing":[197],"competing":[198],"schemes":[199],"four":[202],"metrics":[204],"F1,":[206],"MCC,":[207],"AUROC,":[208],"AUPR.":[210]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-12-03T00:00:00"}
