{"id":"https://openalex.org/W2952522777","doi":"https://doi.org/10.1093/bioinformatics/bty543","title":"NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug\u2013target interactions","display_name":"NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug\u2013target interactions","publication_year":2018,"publication_date":"2018-06-29","ids":{"openalex":"https://openalex.org/W2952522777","doi":"https://doi.org/10.1093/bioinformatics/bty543","mag":"2952522777","pmid":"https://pubmed.ncbi.nlm.nih.gov/30561548"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty543","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty543","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/104/27182907/bty543.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/104/27182907/bty543.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100689470","display_name":"Fang Wan","orcid":"https://orcid.org/0000-0003-1647-3278"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangping Wan","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076008539","display_name":"Lixiang Hong","orcid":"https://orcid.org/0000-0002-4753-7660"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lixiang Hong","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017898444","display_name":"An Xiao","orcid":"https://orcid.org/0000-0003-0909-3234"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"An Xiao","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101911266","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-3833-4498"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Tao Jiang","raw_affiliation_strings":["Bioinformatics Division, BNRIST, Tsinghua University, Beijing, China","Department of Computer Science and Engineering, University of California, Riverside, CA, USA","Department of Computer Science and Technology, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Division, BNRIST, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA, USA","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009826239","display_name":"Jianyang Zeng","orcid":"https://orcid.org/0000-0003-0950-7716"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianyang Zeng","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5009826239"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":22.1975,"has_fulltext":false,"cited_by_count":390,"citation_normalized_percentile":{"value":0.99648465,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"1","first_page":"104","last_page":"111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9807000160217285,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9807000160217285,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00570000009611249,"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":0.002899999963119626,"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/computer-science","display_name":"Computer science","score":0.6893280744552612},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6295475363731384},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5084280371665955},{"id":"https://openalex.org/keywords/information-integration","display_name":"Information integration","score":0.4754447937011719},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41854119300842285},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4126480221748352},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3332173228263855},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3330240845680237},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3180469274520874},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10734575986862183},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.060135722160339355}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6893280744552612},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6295475363731384},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5084280371665955},{"id":"https://openalex.org/C33326189","wikidata":"https://www.wikidata.org/wiki/Q17092450","display_name":"Information integration","level":2,"score":0.4754447937011719},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41854119300842285},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4126480221748352},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3332173228263855},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3330240845680237},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3180469274520874},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10734575986862183},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.060135722160339355},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty543","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty543","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/104/27182907/bty543.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30561548","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30561548","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty543","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty543","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/104/27182907/bty543.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1117163193","display_name":null,"funder_award_id":"IIS-1646333","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6429079033","display_name":"\u57fa\u4e8e\u751f\u7269\u7f51\u7edc\u7684\u75c5\u8bc1\u7ed3\u5408\u7814\u7a76\u65b9\u6cd5","funder_award_id":"81630103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8755943873","display_name":"\u57fa\u4e8e\u7f51\u7edc\u7684\u836f\u7269\uff0d\u9776\u6807\u76f8\u4e92\u4f5c\u7528\u9884\u6d4b\u7684\u6a21\u578b\u7814\u7a76","funder_award_id":"61472205","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320336066","display_name":"Beijing Advanced Innovation Center for Structural Biology, Tsinghua University","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1588586811","https://openalex.org/W1757990252","https://openalex.org/W1965207856","https://openalex.org/W1976526581","https://openalex.org/W1984014392","https://openalex.org/W1988037271","https://openalex.org/W1998898494","https://openalex.org/W2019935345","https://openalex.org/W2029348196","https://openalex.org/W2066201825","https://openalex.org/W2087064593","https://openalex.org/W2105668062","https://openalex.org/W2106029302","https://openalex.org/W2122863289","https://openalex.org/W2123688186","https://openalex.org/W2124001239","https://openalex.org/W2126671570","https://openalex.org/W2137052779","https://openalex.org/W2139736926","https://openalex.org/W2142572836","https://openalex.org/W2153579005","https://openalex.org/W2154718035","https://openalex.org/W2154851992","https://openalex.org/W2161607603","https://openalex.org/W2162011385","https://openalex.org/W2419892062","https://openalex.org/W2471196942","https://openalex.org/W2513544049","https://openalex.org/W2519887557","https://openalex.org/W2540547679","https://openalex.org/W2556131117","https://openalex.org/W2565684601","https://openalex.org/W2610646689","https://openalex.org/W2612690371","https://openalex.org/W2743104969","https://openalex.org/W2753953057","https://openalex.org/W2914059076","https://openalex.org/W2964015378","https://openalex.org/W2964321699","https://openalex.org/W3104097132","https://openalex.org/W4294170691","https://openalex.org/W6682691769","https://openalex.org/W6720006811","https://openalex.org/W6726873649","https://openalex.org/W6730280152"],"related_works":["https://openalex.org/W4206379684","https://openalex.org/W2366105490","https://openalex.org/W2580680567","https://openalex.org/W2606076248","https://openalex.org/W2391251536","https://openalex.org/W2961085424","https://openalex.org/W4285170202","https://openalex.org/W114270996","https://openalex.org/W4249200654","https://openalex.org/W2396656278"],"abstract_inverted_index":{"Motivation:":[0],"Accurately":[1],"predicting":[2],"drug-target":[3],"interactions":[4],"(DTIs)":[5],"in":[6,48,203],"silico":[7],"can":[8,41,181],"guide":[9],"the":[10,26,32,35,64,76,140],"drug":[11,17,165,189,192],"discovery":[12],"process":[13],"and":[14,39,59,73,101,108,159,166,185,191,195,200],"thus":[15],"facilitate":[16,111],"development.":[18],"Computational":[19],"approaches":[20],"for":[21,188],"DTI":[22,112,122],"prediction":[23,81,116,123],"that":[24,34,62,93,179],"adopt":[25],"systems":[27],"biology":[28],"perspective":[29],"generally":[30],"exploit":[31],"rationale":[33],"properties":[36],"of":[37,56,78,106,144,155,157],"drugs":[38,107],"targets":[40,109],"be":[42],"characterized":[43],"by":[44,53],"their":[45],"functional":[46],"roles":[47],"biological":[49],"networks.":[50],"Results:":[51],"Inspired":[52],"recent":[54],"advance":[55],"information":[57,96,169],"passing":[58],"aggregation":[60],"techniques":[61],"generalize":[63],"convolution":[65],"neural":[66],"networks":[67],"to":[68,110,162],"mine":[69],"large-scale":[70],"graph":[71],"data":[72,100,201,212],"greatly":[74],"improve":[75],"performance":[77,117],"many":[79],"network-related":[80],"tasks,":[82],"we":[83],"develop":[84],"a":[85,152,183],"new":[86],"nonlinear":[87],"end-to-end":[88],"learning":[89],"model,":[90],"called":[91],"NeoDTI,":[92],"integrates":[94],"diverse":[95],"from":[97,135],"heterogeneous":[98],"network":[99],"automatically":[102],"learns":[103],"topology-preserving":[104],"representations":[105],"prediction.":[113],"The":[114,197],"substantial":[115],"improvement":[118],"over":[119],"other":[120],"state-of-the-art":[121],"methods":[124],"as":[125,127],"well":[126],"several":[128],"novel":[129],"predicted":[130],"DTIs":[131],"with":[132],"evidence":[133],"supports":[134],"previous":[136],"studies":[137],"have":[138],"demonstrated":[139],"superior":[141],"predictive":[142],"power":[143],"NeoDTI.":[145],"In":[146],"addition,":[147],"NeoDTI":[148,180,204],"is":[149,160],"robust":[150,186],"against":[151],"wide":[153],"range":[154],"choices":[156],"hyperparameters":[158],"ready":[161],"integrate":[163],"more":[164],"target":[167],"related":[168],"(e.g.":[170],"compound-protein":[171],"binding":[172],"affinity":[173],"data).":[174],"All":[175],"these":[176],"results":[177],"suggest":[178],"offer":[182],"powerful":[184],"tool":[187],"development":[190],"repositioning.":[193],"Availability":[194],"implementation:":[196],"source":[198],"code":[199],"used":[202],"are":[205,213],"available":[206,214],"at:":[207],"https://github.com/FangpingWan/NeoDTI.":[208],"Supplementary":[209,211],"information:":[210],"at":[215],"Bioinformatics":[216],"online.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":27},{"year":2025,"cited_by_count":57},{"year":2024,"cited_by_count":76},{"year":2023,"cited_by_count":58},{"year":2022,"cited_by_count":59},{"year":2021,"cited_by_count":56},{"year":2020,"cited_by_count":37},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
