{"id":"https://openalex.org/W4394564327","doi":"https://doi.org/10.1109/jbhi.2024.3384696","title":"Redefining the Game: MVAE-DFDPnet's Low-Dimensional Embeddings for Superior Drug-Protein Interaction Predictions","display_name":"Redefining the Game: MVAE-DFDPnet's Low-Dimensional Embeddings for Superior Drug-Protein Interaction Predictions","publication_year":2024,"publication_date":"2024-04-08","ids":{"openalex":"https://openalex.org/W4394564327","doi":"https://doi.org/10.1109/jbhi.2024.3384696"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3384696","doi":"https://doi.org/10.1109/jbhi.2024.3384696","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3384696","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,"listed_in":["ccf-c","cwts-core","dongbi-a","doyens","jufo-2","ki-jl-2","medline","norway-1","poland-140","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2024/04/01/2024.04.01.587541.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018295220","display_name":"Liang-Yong Xia","orcid":"https://orcid.org/0000-0003-1015-7127","observed_orcids":["https://orcid.org/0000-0003-1015-7127"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang-Yong Xia","raw_affiliation_strings":["Shanghai Jiao Tong University;","National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0003-1015-7127","affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University;","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112586290","display_name":"Yu Xuan Wu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Wu","raw_affiliation_strings":["Princeton University","Center for Statistics and Machine Learning Department of Electrical Engineering Department of Computer Science, Princeton University, Princeton, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Princeton University","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Center for Statistics and Machine Learning Department of Electrical Engineering Department of Computer Science, Princeton University, Princeton, NJ, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030909961","display_name":"Longfei Zhao","orcid":"https://orcid.org/0000-0002-6277-0137","observed_orcids":["https://orcid.org/0000-0002-6277-0137"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Longfei Zhao","raw_affiliation_strings":["Shanghai Jiao Tong University;","National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University;","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055282096","display_name":"Leying Chen","orcid":"https://orcid.org/0000-0002-6448-4177","observed_orcids":["https://orcid.org/0000-0002-6448-4177","https://orcid.org/0009-0000-3477-9073"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Leying Chen","raw_affiliation_strings":["Shanghai Jiao Tong University;","School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University;","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100784918","display_name":"Shiyi Zhang","orcid":"https://orcid.org/0000-0002-9375-5992","observed_orcids":["https://orcid.org/0000-0002-9375-5992"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiyi Zhang","raw_affiliation_strings":["Shanghai Jiao Tong University;","School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University;","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100707460","display_name":"Mengdi Wang","orcid":"https://orcid.org/0000-0002-2101-9507","observed_orcids":["https://orcid.org/0000-0002-2101-9507","https://orcid.org/0000-0003-0841-2651","https://orcid.org/0000-0003-4230-1365","https://orcid.org/0000-0001-5407-0416","https://orcid.org/0000-0001-9564-8624","https://orcid.org/0000-0002-3094-7735","https://orcid.org/0000-0002-7658-3797","https://orcid.org/0000-0003-1860-7815"]},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mengdi Wang","raw_affiliation_strings":["Princeton University","Center for Statistics and Machine Learning Department of Electrical Engineering Department of Computer Science, Princeton University, Princeton, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Princeton University","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Center for Statistics and Machine Learning Department of Electrical Engineering Department of Computer Science, Princeton University, Princeton, NJ, USA","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":null,"display_name":"Jie Luo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jie Luo","raw_affiliation_strings":["Shanghai Jiao Tong University;","National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University;","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":{"value":2495,"currency":"USD","value_usd":2495},"apc_paid":null,"fwci":0.4046,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51607936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"28","issue":"7","first_page":"4317","last_page":"4324"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.003700000001117587,"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":0.0010999999940395355,"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/drug-protein-interaction-prediction","display_name":"drug-protein interaction prediction","score":0.9369999766349792},{"id":"https://openalex.org/keywords/deep-forest","display_name":"deep forest","score":0.7739999890327454},{"id":"https://openalex.org/keywords/low-dimensional-embedding","display_name":"low-dimensional embedding","score":0.8899999856948853},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"drug discovery","score":0.5540000200271606},{"id":"https://openalex.org/keywords/t-sne-clustering","display_name":"t-SNE clustering","score":0.5870000123977661}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6234659552574158},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5631145238876343},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.5529853105545044},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5185278654098511},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5006253719329834},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16906210780143738},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15660834312438965},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07635802030563354},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2024.3384696","doi":"https://doi.org/10.1109/jbhi.2024.3384696","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3384696","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,"listed_in":["ccf-c","cwts-core","dongbi-a","doyens","jufo-2","ki-jl-2","medline","norway-1","poland-140","russia-white-list-1","vabb-shw"],"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":"doi:10.1101/2024.04.01.587541","doi":"https://doi.org/10.1101/2024.04.01.587541","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.04.01.587541","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2024/04/01/2024.04.01.587541.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2024.04.01.587541","doi":"https://doi.org/10.1101/2024.04.01.587541","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2024.04.01.587541","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2024/04/01/2024.04.01.587541.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.8048999905586243,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G8733944229","display_name":null,"funder_award_id":"62101321","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8959763610","display_name":null,"funder_award_id":"2020M671125","funder_id":"https://openalex.org/F4320335443","funder_display_name":"Postdoctoral Research 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/F4320335443","display_name":"Postdoctoral Research Foundation of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4394564327.pdf","grobid_xml":"https://content.openalex.org/works/W4394564327.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1875842236","https://openalex.org/W1978400666","https://openalex.org/W1998898494","https://openalex.org/W2007436490","https://openalex.org/W2029335938","https://openalex.org/W2057195902","https://openalex.org/W2058501113","https://openalex.org/W2063280109","https://openalex.org/W2105668062","https://openalex.org/W2135007932","https://openalex.org/W2135209350","https://openalex.org/W2139736926","https://openalex.org/W2145578524","https://openalex.org/W2147241078","https://openalex.org/W2159027272","https://openalex.org/W2162011385","https://openalex.org/W2170344111","https://openalex.org/W2259538443","https://openalex.org/W2267547839","https://openalex.org/W2280793526","https://openalex.org/W2583911935","https://openalex.org/W2586637063","https://openalex.org/W2592340788","https://openalex.org/W2607497028","https://openalex.org/W2611702131","https://openalex.org/W2753953057","https://openalex.org/W2767891136","https://openalex.org/W2772309359","https://openalex.org/W2793951981","https://openalex.org/W2803462582","https://openalex.org/W2890507936","https://openalex.org/W2900090807","https://openalex.org/W2924530200","https://openalex.org/W2940010972","https://openalex.org/W2945027804","https://openalex.org/W2952522777","https://openalex.org/W2953544853","https://openalex.org/W2969324283","https://openalex.org/W2986115017","https://openalex.org/W2987928072","https://openalex.org/W2989747508","https://openalex.org/W2989919747","https://openalex.org/W2999304916","https://openalex.org/W3003038853","https://openalex.org/W3036006967","https://openalex.org/W3095380161","https://openalex.org/W3107527779","https://openalex.org/W3107626709","https://openalex.org/W3112376646","https://openalex.org/W3112600195","https://openalex.org/W3120392574","https://openalex.org/W3217681006","https://openalex.org/W4210717126","https://openalex.org/W4210842338","https://openalex.org/W4220788456","https://openalex.org/W4248234957","https://openalex.org/W4297358906","https://openalex.org/W4307432689","https://openalex.org/W4315645662","https://openalex.org/W4319321503"],"related_works":["https://openalex.org/W4385809304","https://openalex.org/W4394997844","https://openalex.org/W4306160672","https://openalex.org/W7131876938","https://openalex.org/W4367297900","https://openalex.org/W4214530112","https://openalex.org/W3177337660","https://openalex.org/W4386820955","https://openalex.org/W4390991955","https://openalex.org/W4391789154"],"abstract_inverted_index":{"Precisely":[0],"predicting":[1,123],"drug-protein":[2],"interactions":[3,124],"(DPIs)":[4],"is":[5,20,115],"pivotal":[6],"for":[7,58],"drug":[8,27,77,130],"discovery":[9],"and":[10,23,28,60,79,91,129,152],"advancing":[11],"precision":[12],"medicine.":[13],"A":[14],"significant":[15],"challenge":[16],"in":[17,107,122],"this":[18],"domain":[19],"the":[21,88,144],"high-dimensional":[22],"heterogeneous":[24],"data":[25],"characterizing":[26],"protein":[29,80],"attributes,":[30],"along":[31],"with":[32,140],"their":[33],"intricate":[34],"interactions.":[35],"In":[36],"our":[37,63,94,97],"study,":[38],"we":[39,133],"introduce":[40],"a":[41,49],"novel":[42,126],"deep":[43],"learning":[44],"architecture:":[45],"theMulti-viewVariationalAuto-Encoder":[46],"embedded":[47],"within":[48],"cascadeDeepForest":[50],"(MVAE-DFDPnet).":[51],"This":[52],"framework":[53],"adeptly":[54],"learns":[55],"ultra-low-dimensional":[56,83],"embedding":[57,69,84],"drugs":[59],"proteins.":[61],"Notably,":[62],"t-SNE":[64],"analysis":[65],"reveals":[66],"that":[67],"two-dimensional":[68],"can":[70,156],"clearly":[71],"define":[72],"clusters":[73],"corresponding":[74],"to":[75,87,150],"diverse":[76],"classes":[78],"families.":[81],"These":[82],"likely":[85],"contribute":[86],"enhanced":[89],"robustness":[90],"generalizability":[92],"of":[93],"MVAE-DFDPnet.":[95],"Impressively,":[96],"model":[98],"surpasses":[99],"current":[100],"leading":[101],"methods":[102],"on":[103],"benchmark":[104],"datasets,":[105],"functioning":[106],"significantly":[108],"reduced":[109],"dimensional":[110],"spaces.":[111],"The":[112,147],"model's":[113],"resilience":[114],"further":[116],"evidenced":[117],"by":[118],"its":[119],"sustained":[120],"accuracy":[121],"involving":[125],"drugs,":[127],"proteins,":[128],"classes.":[131],"Additionally,":[132],"have":[134],"corroborated":[135],"several":[136],"newly":[137],"identified":[138],"DPIs":[139],"experimental":[141],"evidence":[142],"from":[143],"scientific":[145],"literature.":[146],"code":[148],"used":[149],"generate":[151],"analyze":[153],"these":[154],"results":[155],"be":[157],"accessed":[158],"fromhttps://github.com/Macau-LYXia/MVAE-DFDPnet-V2.":[159]},"counts_by_year":[{"year":2024,"cited_by_count":3}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2024-04-09T00:00:00"}
