{"id":"https://openalex.org/W4403216757","doi":"https://doi.org/10.1080/24751839.2024.2411883","title":"Combining handcrafted and learned features using deep learning to improve protein-protein interaction prediction performance","display_name":"Combining handcrafted and learned features using deep learning to improve protein-protein interaction prediction performance","publication_year":2024,"publication_date":"2024-10-08","ids":{"openalex":"https://openalex.org/W4403216757","doi":"https://doi.org/10.1080/24751839.2024.2411883"},"language":"en","primary_location":{"id":"doi:10.1080/24751839.2024.2411883","is_oa":true,"landing_page_url":"https://doi.org/10.1080/24751839.2024.2411883","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/24751839.2024.2411883?needAccess=true","source":{"id":"https://openalex.org/S4210226961","display_name":"Journal of Information and Telecommunication","issn_l":"2475-1839","issn":["2475-1839","2475-1847"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Information and Telecommunication","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.tandfonline.com/doi/pdf/10.1080/24751839.2024.2411883?needAccess=true","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107822044","display_name":"Tran Hoai Nhan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095101","display_name":"Hue University","ror":"https://ror.org/00qaa6j11","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210095101"]},{"id":"https://openalex.org/I4210141768","display_name":"Hue University of Education","ror":"https://ror.org/04bm3wy68","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210141768"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Tran Hoai Nhan","raw_affiliation_strings":["Department of Informatics, University of Education, Hue University","Department of Informatics, University of Education, Hue University, Hue city, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Education, Hue University","institution_ids":["https://openalex.org/I4210141768","https://openalex.org/I4210095101"]},{"raw_affiliation_string":"Department of Informatics, University of Education, Hue University, Hue city, Vietnam","institution_ids":["https://openalex.org/I4210095101"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113422959","display_name":"Nguyen Phuc Xuan Quynh","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095101","display_name":"Hue University","ror":"https://ror.org/00qaa6j11","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210095101"]},{"id":"https://openalex.org/I4210141768","display_name":"Hue University of Education","ror":"https://ror.org/04bm3wy68","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210141768"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Nguyen Phuc Xuan Quynh","raw_affiliation_strings":["Department of Informatics, University of Education, Hue University","Department of Informatics, University of Education, Hue University, Hue city, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Education, Hue University","institution_ids":["https://openalex.org/I4210141768","https://openalex.org/I4210095101"]},{"raw_affiliation_string":"Department of Informatics, University of Education, Hue University, Hue city, Vietnam","institution_ids":["https://openalex.org/I4210095101"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012362786","display_name":"L\u00ea Anh Ph\u01b0\u01a1ng","orcid":"https://orcid.org/0000-0001-9514-9550"},"institutions":[{"id":"https://openalex.org/I4210095101","display_name":"Hue University","ror":"https://ror.org/00qaa6j11","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210095101"]},{"id":"https://openalex.org/I4210141768","display_name":"Hue University of Education","ror":"https://ror.org/04bm3wy68","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210141768"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Le Anh Phuong","raw_affiliation_strings":["Department of Informatics, University of Education, Hue University","Department of Informatics, University of Education, Hue University, Hue city, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Education, Hue University","institution_ids":["https://openalex.org/I4210141768","https://openalex.org/I4210095101"]},{"raw_affiliation_string":"Department of Informatics, University of Education, Hue University, Hue city, Vietnam","institution_ids":["https://openalex.org/I4210095101"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5012362786","https://openalex.org/A5107822044"],"corresponding_institution_ids":["https://openalex.org/I4210095101","https://openalex.org/I4210141768"],"apc_list":{"value":925,"currency":"GBP","value_usd":1134},"apc_paid":{"value":925,"currency":"GBP","value_usd":1134},"fwci":0.1866,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.54502177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"9","issue":"2","first_page":"151","last_page":"172"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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":0.9975000023841858,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9973000288009644,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.5823414325714111},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5724356770515442},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.508768618106842},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4616059362888336}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5823414325714111},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5724356770515442},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.508768618106842},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4616059362888336}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1080/24751839.2024.2411883","is_oa":true,"landing_page_url":"https://doi.org/10.1080/24751839.2024.2411883","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/24751839.2024.2411883?needAccess=true","source":{"id":"https://openalex.org/S4210226961","display_name":"Journal of Information and Telecommunication","issn_l":"2475-1839","issn":["2475-1839","2475-1847"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Information and Telecommunication","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:141e769df7c14db4a5bdebbf58db0c9c","is_oa":true,"landing_page_url":"https://doaj.org/article/141e769df7c14db4a5bdebbf58db0c9c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Information and Telecommunication, Vol 9, Iss 2, Pp 151-172 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1080/24751839.2024.2411883","is_oa":true,"landing_page_url":"https://doi.org/10.1080/24751839.2024.2411883","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/24751839.2024.2411883?needAccess=true","source":{"id":"https://openalex.org/S4210226961","display_name":"Journal of Information and Telecommunication","issn_l":"2475-1839","issn":["2475-1839","2475-1847"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Information and Telecommunication","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403216757.pdf","grobid_xml":"https://content.openalex.org/works/W4403216757.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W168564468","https://openalex.org/W1522301498","https://openalex.org/W1614298861","https://openalex.org/W1836465849","https://openalex.org/W1886978693","https://openalex.org/W1981091069","https://openalex.org/W1982267716","https://openalex.org/W1985919127","https://openalex.org/W1993711987","https://openalex.org/W2044523575","https://openalex.org/W2101234009","https://openalex.org/W2114358087","https://openalex.org/W2132292391","https://openalex.org/W2132582966","https://openalex.org/W2139237500","https://openalex.org/W2152705149","https://openalex.org/W2156125289","https://openalex.org/W2158714788","https://openalex.org/W2162392441","https://openalex.org/W2187089797","https://openalex.org/W2340589369","https://openalex.org/W2402144811","https://openalex.org/W2493916176","https://openalex.org/W2524367868","https://openalex.org/W2547150868","https://openalex.org/W2616246685","https://openalex.org/W2618265628","https://openalex.org/W2735435042","https://openalex.org/W2744103888","https://openalex.org/W2768348081","https://openalex.org/W2789600509","https://openalex.org/W2804331675","https://openalex.org/W2890911678","https://openalex.org/W2911614559","https://openalex.org/W2950389803","https://openalex.org/W2952253955","https://openalex.org/W2995514860","https://openalex.org/W2997318833","https://openalex.org/W3079352602","https://openalex.org/W3112376646","https://openalex.org/W3118577024","https://openalex.org/W3124662554","https://openalex.org/W3138032944","https://openalex.org/W3153990350","https://openalex.org/W3155739706","https://openalex.org/W3188235934","https://openalex.org/W4316465078","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W4321369474","https://openalex.org/W4360585206","https://openalex.org/W4285208911","https://openalex.org/W3046775127","https://openalex.org/W3082895349"],"abstract_inverted_index":{"Understanding":[0],"protein-protein":[1],"interactions":[2,177],"(PPIs)":[3],"is":[4,158],"essential":[5],"because":[6],"knowledge":[7],"regarding":[8],"PPIs":[9],"helps":[10],"in":[11,20,67,178],"determining":[12],"the":[13,83,130,145,153,168],"biochemical":[14],"functions":[15],"of":[16,117,155],"organisms.":[17],"Advances":[18],"made":[19],"machine":[21],"learning":[22],"techniques,":[23],"for":[24,191],"example,":[25],"DeepFE-PPI,":[26],"GcForest-PPI,":[27],"and":[28,71,101,123,141,148,163,183,189],"DeepPPI,":[29],"have":[30],"been":[31],"applied":[32],"to":[33,60,76,128],"enhance":[34],"PPI":[35,54,78,184],"prediction":[36],"performance.":[37,56],"However,":[38],"most":[39],"methods":[40,122],"use":[41],"either":[42],"handcrafted":[43,70,84],"or":[44],"learned":[45,72,104],"features.":[46],"Improving":[47],"protein":[48,118],"representation":[49],"quality":[50],"can":[51],"significantly":[52],"impact":[53],"model":[55,138,157],"This":[57],"study":[58],"aims":[59],"propose":[61],"a":[62,114],"deep":[63],"neural":[64],"network-based":[65],"model,":[66],"which":[68],"both":[69],"features":[73,85,105],"are":[74,86,106,126,194],"fused":[75],"improve":[77],"prediction.":[79],"In":[80],"our":[81,137,156,164],"method,":[82],"computed":[87],"by":[88,108],"sequence":[89],"descriptors,":[90],"including":[91,181],"Amino":[92],"Acid":[93],"Composition":[94],"(AAC),":[95],"Local":[96],"Descriptors,":[97],"Pseudo-AAC,":[98,100],"Amphiphilic":[99],"Quasi-Sequence-Order.":[102],"The":[103,133,186],"generated":[107],"Word2vec":[109],"after":[110],"being":[111],"trained":[112],"on":[113,144],"large":[115],"database":[116],"sequences.":[119],"Standard":[120],"evaluation":[121],"benchmark":[124],"datasets":[125],"used":[127],"assess":[129],"proposed":[131,169],"model.":[132],"results":[134],"show":[135],"that":[136,167],"achieves":[139],"95.8%":[140],"99.3%":[142],"accuracy":[143],"Saccharomyces":[146],"cerevisiae":[147],"Human":[149],"datasets,":[150,180],"respectively.":[151],"Additionally,":[152],"generalizability":[154],"evaluated":[159],"through":[160],"independent":[161],"tests,":[162],"findings":[165],"indicate":[166],"feature":[170],"combination":[171],"method":[172],"correctly":[173],"classifies":[174],"experimentally":[175],"validated":[176],"eight":[179],"cross-species":[182],"networks.":[185],"source":[187],"code":[188],"data":[190],"this":[192],"work":[193],"included":[195],"at":[196],"https://github.com/npxquynhdhsp/ComFeatPPI.git.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
