{"id":"https://openalex.org/W4410886857","doi":"https://doi.org/10.1109/jbhi.2025.3575429","title":"PCLT-PPI: Predicting Multi-Type Interactions Between Proteins Based on Point Cloud Structure and Local Topology Preservation","display_name":"PCLT-PPI: Predicting Multi-Type Interactions Between Proteins Based on Point Cloud Structure and Local Topology Preservation","publication_year":2025,"publication_date":"2025-05-30","ids":{"openalex":"https://openalex.org/W4410886857","doi":"https://doi.org/10.1109/jbhi.2025.3575429","pmid":"https://pubmed.ncbi.nlm.nih.gov/40445810"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3575429","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3575429","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","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/A5100780138","display_name":"Minglei Li","orcid":"https://orcid.org/0000-0002-8618-954X"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minglei Li","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023247075","display_name":"Yonghong Hou","orcid":"https://orcid.org/0000-0002-1676-5505"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yurui Hou","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079448948","display_name":"Shuqin Wang","orcid":"https://orcid.org/0000-0003-4873-1307"},"institutions":[{"id":"https://openalex.org/I15062923","display_name":"Tianjin Normal University","ror":"https://ror.org/05x2td559","country_code":"CN","type":"education","lineage":["https://openalex.org/I15062923"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuqin Wang","raw_affiliation_strings":["College of Computer and Information Engineering, Tianjin Normal University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer and Information Engineering, Tianjin Normal University, Tianjin, China","institution_ids":["https://openalex.org/I15062923"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037600606","display_name":"Jinmao Wei","orcid":"https://orcid.org/0000-0003-0809-6687"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinmao Wei","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100414608","display_name":"Jian Liu","orcid":"https://orcid.org/0000-0001-5516-0157"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Liu","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100780138"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":null,"apc_paid":null,"fwci":1.6374,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.85881863,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"29","issue":"10","first_page":"7753","last_page":"7762"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.8601999878883362,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.8601999878883362,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.8438000082969666,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.7748000025749207,"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/topology","display_name":"Topology (electrical circuits)","score":0.6730707883834839},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.622343897819519},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.5435831546783447},{"id":"https://openalex.org/keywords/point-cloud","display_name":"Point cloud","score":0.49400025606155396},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4708119332790375},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.4532237946987152},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1769580841064453},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16597244143486023},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08142894506454468}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.6730707883834839},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.622343897819519},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.5435831546783447},{"id":"https://openalex.org/C131979681","wikidata":"https://www.wikidata.org/wiki/Q1899648","display_name":"Point cloud","level":2,"score":0.49400025606155396},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4708119332790375},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.4532237946987152},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1769580841064453},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16597244143486023},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08142894506454468},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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":"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":"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":"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":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":"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":"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":"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},{"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/jbhi.2025.3575429","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3575429","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40445810","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40445810","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/13","display_name":"Climate action"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1976526581","https://openalex.org/W1976937534","https://openalex.org/W1977186059","https://openalex.org/W1980831278","https://openalex.org/W1982267716","https://openalex.org/W2029476889","https://openalex.org/W2102245393","https://openalex.org/W2152705149","https://openalex.org/W2157825442","https://openalex.org/W2342374505","https://openalex.org/W2405065882","https://openalex.org/W2617750324","https://openalex.org/W2739455021","https://openalex.org/W2753953057","https://openalex.org/W2885583144","https://openalex.org/W2890911678","https://openalex.org/W2900569176","https://openalex.org/W2945669687","https://openalex.org/W2957436444","https://openalex.org/W3005769002","https://openalex.org/W3045012301","https://openalex.org/W3087769169","https://openalex.org/W3134169372","https://openalex.org/W3135883064","https://openalex.org/W3177828909","https://openalex.org/W3189432583","https://openalex.org/W3192988454","https://openalex.org/W3205586691","https://openalex.org/W3216616254","https://openalex.org/W3217568487","https://openalex.org/W4224291667","https://openalex.org/W4290712920","https://openalex.org/W4294170691","https://openalex.org/W4317867801","https://openalex.org/W4321851522","https://openalex.org/W4375928910"],"related_works":["https://openalex.org/W4244478748","https://openalex.org/W3150465815","https://openalex.org/W4223488648","https://openalex.org/W2134969820","https://openalex.org/W2251605416","https://openalex.org/W1997222214","https://openalex.org/W2560439919","https://openalex.org/W4389340727","https://openalex.org/W2802581102","https://openalex.org/W4205786897"],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1],"(PPIs)":[2],"play":[3],"a":[4,69,187],"crucial":[5],"role":[6],"in":[7,112],"cellular":[8,19],"biochemical":[9],"reactions.":[10],"Computationally":[11],"mining":[12],"PPI":[13,70,146,181],"can":[14,179],"help":[15],"us":[16],"better":[17,142],"understand":[18],"regulatory":[20],"mechanisms.":[21],"Most":[22],"existing":[23],"methods":[24],"focus":[25],"on":[26,39,74],"the":[27,33,52,57,64,103,107],"linear":[28],"structure":[29,38,78,174],"of":[30,35,110],"proteins,":[31],"ignoring":[32],"influence":[34],"native":[36],"spatial":[37],"their":[40,113],"properties.":[41],"Furthermore,":[42],"when":[43,150],"neural":[44,100],"networks":[45],"are":[46,155],"used":[47],"to":[48],"learn":[49],"protein":[50,75,91,152],"embeddings,":[51],"nonlinear":[53],"transformations":[54],"may":[55,185],"change":[56],"topological":[58],"relationships":[59],"between":[60],"proteins.":[61],"To":[62],"address":[63],"above":[65],"issues,":[66],"we":[67],"propose":[68],"prediction":[71,147,182],"method":[72],"based":[73],"point":[76,92,172],"cloud":[77,93,173],"and":[79,95,115,131,163,175],"local":[80,108,176],"topology":[81,109,177],"preservation,":[82],"naming":[83],"it":[84],"PCLT-PPI.":[85],"It":[86],"extracts":[87],"structural":[88],"features":[89,97],"from":[90],"structures":[94],"relational":[96],"through":[98],"graph":[99],"networks.":[101],"Throughout":[102],"process,":[104],"PCLT-PPI":[105,140],"maintains":[106],"proteins":[111],"origin":[114],"embedding":[116],"spaces.":[117],"Experimental":[118],"results":[119,168],"show":[120],"that,":[121],"under":[122],"three":[123],"test":[124],"set":[125],"partition":[126],"modes":[127],"(Random,":[128],"BFS,":[129],"DFS)":[130],"four":[132],"evaluation":[133],"metrics":[134],"(F1,":[135],"AUC,":[136],"AUPR,":[137],"Hamming":[138],"Loss),":[139],"performs":[141],"than":[143],"several":[144],"state-of-the-art":[145],"methods,":[148],"especially":[149],"predicting":[151],"PPIs":[153],"that":[154,171],"not":[156],"visible":[157],"during":[158],"training,":[159],"exhibiting":[160],"stronger":[161],"robustness":[162],"higher":[164],"generalization":[165],"ability.":[166],"The":[167],"also":[169],"demonstrate":[170],"preservation":[178],"improve":[180],"performance,":[183],"which":[184],"provide":[186],"reference":[188],"for":[189],"subsequent":[190],"related":[191],"research.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
