{"id":"https://openalex.org/W4401019921","doi":"https://doi.org/10.1021/acs.jcim.4c01070","title":"HPTRMF: Collaborative Matrix Factorization-Based Prediction Method for LncRNA-Disease Associations Using High-Order Perturbation and Flexible Trifactor Regularization","display_name":"HPTRMF: Collaborative Matrix Factorization-Based Prediction Method for LncRNA-Disease Associations Using High-Order Perturbation and Flexible Trifactor Regularization","publication_year":2024,"publication_date":"2024-07-26","ids":{"openalex":"https://openalex.org/W4401019921","doi":"https://doi.org/10.1021/acs.jcim.4c01070","pmid":"https://pubmed.ncbi.nlm.nih.gov/39058598"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01070","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01070","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":"https://openalex.org/A5100889022","display_name":"Guobo Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guobo Xie","raw_affiliation_strings":["School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China","institution_ids":["https://openalex.org/I139024713"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109753400","display_name":"Dayin Li","orcid":null},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dayin Li","raw_affiliation_strings":["School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China"],"raw_orcid":"https://orcid.org/0009-0006-6266-1500","affiliations":[{"raw_affiliation_string":"School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China","institution_ids":["https://openalex.org/I139024713"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044845314","display_name":"Zhiyi Lin","orcid":"https://orcid.org/0000-0002-3464-3472"},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhiyi Lin","raw_affiliation_strings":["School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China","institution_ids":["https://openalex.org/I139024713"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102791675","display_name":"Guosheng Gu","orcid":"https://orcid.org/0000-0002-0446-8255"},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guosheng Gu","raw_affiliation_strings":["School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China","institution_ids":["https://openalex.org/I139024713"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114185796","display_name":"Weijun Li","orcid":null},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weijun Li","raw_affiliation_strings":["School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China","institution_ids":["https://openalex.org/I139024713"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013466748","display_name":"Ruibin Chen","orcid":"https://orcid.org/0000-0001-9215-1129"},"institutions":[{"id":"https://openalex.org/I139024713","display_name":"Guangdong University of Technology","ror":"https://ror.org/04azbjn80","country_code":"CN","type":"education","lineage":["https://openalex.org/I139024713"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruibin Chen","raw_affiliation_strings":["School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Guangdong University of Technology, Guangzhou 510006, China","institution_ids":["https://openalex.org/I139024713"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100448059","display_name":"Zhenguo Liu","orcid":"https://orcid.org/0000-0002-2668-0724"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210128921","display_name":"The First Affiliated Hospital, Sun Yat-sen University","ror":"https://ror.org/037p24858","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128921"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenguo Liu","raw_affiliation_strings":["2MD Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2MD Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China","institution_ids":["https://openalex.org/I4210128921","https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5044845314","https://openalex.org/A5102791675"],"corresponding_institution_ids":["https://openalex.org/I139024713"],"apc_list":null,"apc_paid":null,"fwci":2.1682,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.88241318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"64","issue":"24","first_page":"9594","last_page":"9608"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9797000288963318,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11765","display_name":"Circular RNAs in diseases","score":0.9596999883651733,"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/regularization","display_name":"Regularization (linguistics)","score":0.7121068835258484},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6529709100723267},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.6262105703353882},{"id":"https://openalex.org/keywords/factorization","display_name":"Factorization","score":0.4858541190624237},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46189889311790466},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.4403463304042816},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4325549006462097},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.41914427280426025},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3525826632976532},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34834223985671997},{"id":"https://openalex.org/keywords/eigenvalues-and-eigenvectors","display_name":"Eigenvalues and eigenvectors","score":0.07442891597747803}],"concepts":[{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.7121068835258484},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6529709100723267},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.6262105703353882},{"id":"https://openalex.org/C187834632","wikidata":"https://www.wikidata.org/wiki/Q188804","display_name":"Factorization","level":2,"score":0.4858541190624237},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46189889311790466},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.4403463304042816},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4325549006462097},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.41914427280426025},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3525826632976532},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34834223985671997},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.07442891597747803},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c01070","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01070","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:39058598","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39058598","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":[{"score":0.6000000238418579,"display_name":"Climate action","id":"https://metadata.un.org/sdg/13"}],"awards":[{"id":"https://openalex.org/G1331630691","display_name":null,"funder_award_id":"62002070","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4854394195","display_name":null,"funder_award_id":"202102021236","funder_id":"https://openalex.org/F4320317327","funder_display_name":"Scientific and Technological Planning Project of Guangzhou City"},{"id":"https://openalex.org/G4938215705","display_name":null,"funder_award_id":"82001331","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320317327","display_name":"Scientific and Technological Planning Project of Guangzhou City","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1511814458","https://openalex.org/W2029348196","https://openalex.org/W2080131995","https://openalex.org/W2127818057","https://openalex.org/W2128983843","https://openalex.org/W2141222510","https://openalex.org/W2152970345","https://openalex.org/W2288381231","https://openalex.org/W2462108616","https://openalex.org/W2891866117","https://openalex.org/W2912626494","https://openalex.org/W2953008627","https://openalex.org/W2980526638","https://openalex.org/W3006715646","https://openalex.org/W3014082018","https://openalex.org/W3016216710","https://openalex.org/W3091358760","https://openalex.org/W3120801559","https://openalex.org/W3162698679","https://openalex.org/W3168486775","https://openalex.org/W3208264599","https://openalex.org/W4206904133","https://openalex.org/W4223590848","https://openalex.org/W4225763981","https://openalex.org/W4287958536","https://openalex.org/W4295241431","https://openalex.org/W4297183296","https://openalex.org/W4297474196","https://openalex.org/W4302362948","https://openalex.org/W4306732347","https://openalex.org/W4315650815","https://openalex.org/W4321194906","https://openalex.org/W4321201797","https://openalex.org/W4361275221","https://openalex.org/W4386056585","https://openalex.org/W4389918314","https://openalex.org/W4390563851","https://openalex.org/W4391708443","https://openalex.org/W4392094009","https://openalex.org/W4392111029","https://openalex.org/W4392571650","https://openalex.org/W4394014430","https://openalex.org/W4394619651","https://openalex.org/W4394749617"],"related_works":["https://openalex.org/W2794559785","https://openalex.org/W1754499339","https://openalex.org/W2013873776","https://openalex.org/W2950281908","https://openalex.org/W2963117165","https://openalex.org/W2084977674","https://openalex.org/W2583828359","https://openalex.org/W2119556180","https://openalex.org/W1973739845","https://openalex.org/W119752240"],"abstract_inverted_index":{"Existing":[0],"matrix":[1,38,53],"factorization":[2,39],"methods":[3],"face":[4],"challenges,":[5],"including":[6],"the":[7,55,65,90,103,109],"cold":[8,66],"start":[9,67],"problem":[10,68],"and":[11,28,44,87,121,130],"global":[12,94],"nonlinear":[13,95],"data":[14,71,96,101,128,131],"loss":[15,97],"during":[16],"similarity":[17,83,104],"learning,":[18],"particularly":[19],"in":[20,102,117,135],"predicting":[21],"associations":[22],"between":[23],"long":[24],"noncoding":[25],"RNAs":[26],"(LncRNAs)":[27],"diseases.":[29],"To":[30],"overcome":[31],"these":[32],"issues,":[33],"we":[34],"introduce":[35],"HPTRMF,":[36],"a":[37,50,76],"approach":[40],"incorporating":[41],"high-order":[42,51,60],"perturbation":[43,61],"flexible":[45,77],"trifactor":[46,78],"regularization.":[47],"HPTRMF":[48,74,112],"constructs":[49],"correlation":[52],"utilizing":[54],"known":[56],"association":[57],"matrix,":[58],"leveraging":[59],"to":[62,81],"effectively":[63],"address":[64],"caused":[69],"by":[70,98],"sparsity.":[72],"Additionally,":[73],"incorporates":[75],"regularization":[79],"term":[80],"capture":[82],"information":[84],"on":[85,126],"LncRNAs":[86],"diseases,":[88],"enabling":[89],"effective":[91],"handling":[92],"of":[93,111],"capturing":[99],"such":[100],"matrix.":[105],"Experimental":[106],"results":[107],"demonstrate":[108],"superiority":[110],"over":[113],"nine":[114],"state-of-the-art":[115],"algorithms":[116],"Leave-One-Out":[118],"Cross-Validation":[119,123],"(LOOCV)":[120],"Five-Fold":[122],"(5-Fold":[124],"CV)":[125],"three":[127],"sets.HPTRMF":[129],"sets":[132],"are":[133],"available":[134],"https://github.com/Llvvvv/HPTRMF.":[136]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
