{"id":"https://openalex.org/W4412495848","doi":"https://doi.org/10.1186/s12859-025-06141-0","title":"DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit","display_name":"DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit","publication_year":2025,"publication_date":"2025-07-20","ids":{"openalex":"https://openalex.org/W4412495848","doi":"https://doi.org/10.1186/s12859-025-06141-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/40685357"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06141-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06141-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06141-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06141-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010943369","display_name":"Kavipriya Gananathan","orcid":"https://orcid.org/0000-0002-8604-5634"},"institutions":[{"id":"https://openalex.org/I876193797","display_name":"Vellore Institute of Technology University","ror":"https://ror.org/00qzypv28","country_code":"IN","type":"education","lineage":["https://openalex.org/I876193797"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Kavipriya Gananathan","raw_affiliation_strings":["School of Computer Science Engineering (SCOPE), Vellore Institute of Technology, Chennai, 600127, India. kavipriya.g@vit.ac.in"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science Engineering (SCOPE), Vellore Institute of Technology, Chennai, 600127, India. kavipriya.g@vit.ac.in","institution_ids":["https://openalex.org/I876193797"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113496484","display_name":"D. Manjula","orcid":null},"institutions":[{"id":"https://openalex.org/I876193797","display_name":"Vellore Institute of Technology University","ror":"https://ror.org/00qzypv28","country_code":"IN","type":"education","lineage":["https://openalex.org/I876193797"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"D. Manjula","raw_affiliation_strings":["School of Computer Science Engineering (SCOPE), Vellore Institute of Technology, Chennai, 600127, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science Engineering (SCOPE), Vellore Institute of Technology, Chennai, 600127, India","institution_ids":["https://openalex.org/I876193797"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080285200","display_name":"Vijayan Sugumaran","orcid":"https://orcid.org/0000-0003-2557-3182"},"institutions":[{"id":"https://openalex.org/I177721651","display_name":"Oakland University","ror":"https://ror.org/01ythxj32","country_code":"US","type":"education","lineage":["https://openalex.org/I177721651"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijayan Sugumaran","raw_affiliation_strings":["Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, 48309, USA","Department of Decision and Information Sciences, School of Business Administration, Oakland University, Rochester, MI, 48309, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, 48309, USA","institution_ids":["https://openalex.org/I177721651"]},{"raw_affiliation_string":"Department of Decision and Information Sciences, School of Business Administration, Oakland University, Rochester, MI, 48309, USA","institution_ids":["https://openalex.org/I177721651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17145686,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"185","last_page":"185"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.984499990940094,"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":0.984499990940094,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.002199999988079071,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0019000000320374966,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5623846650123596},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.5202744603157043},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4906965494155884},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4444185495376587},{"id":"https://openalex.org/keywords/unit","display_name":"Unit (ring theory)","score":0.44158506393432617},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43903109431266785},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3581300675868988},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.31605273485183716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29211586713790894},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.2859608232975006},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15413624048233032},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12883692979812622},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10535994172096252},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09584501385688782}],"concepts":[{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5623846650123596},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.5202744603157043},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4906965494155884},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4444185495376587},{"id":"https://openalex.org/C122637931","wikidata":"https://www.wikidata.org/wiki/Q118084","display_name":"Unit (ring theory)","level":2,"score":0.44158506393432617},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43903109431266785},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3581300675868988},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.31605273485183716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29211586713790894},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.2859608232975006},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15413624048233032},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12883692979812622},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10535994172096252},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09584501385688782},{"id":"https://openalex.org/C145420912","wikidata":"https://www.wikidata.org/wiki/Q853077","display_name":"Mathematics education","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"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":"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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06141-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06141-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06141-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40685357","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40685357","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:363f124c36ed425b92178d721640ca21","is_oa":true,"landing_page_url":"https://doaj.org/article/363f124c36ed425b92178d721640ca21","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":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-23 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12278605","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12278605","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06141-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06141-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06141-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320319346","display_name":"Vellore Institute of Technology, Chennai","ror":null},{"id":"https://openalex.org/F4320322838","display_name":"VIT University","ror":"https://ror.org/00qzypv28"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412495848.pdf","grobid_xml":"https://content.openalex.org/works/W4412495848.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W2161323541","https://openalex.org/W2417990257","https://openalex.org/W2754595644","https://openalex.org/W2770261575","https://openalex.org/W2785947426","https://openalex.org/W2814412793","https://openalex.org/W2889165715","https://openalex.org/W2889321024","https://openalex.org/W2899788782","https://openalex.org/W2912469071","https://openalex.org/W2998445959","https://openalex.org/W3000043291","https://openalex.org/W3012994592","https://openalex.org/W3021338900","https://openalex.org/W3084084616","https://openalex.org/W3093358807","https://openalex.org/W3096561213","https://openalex.org/W3162048269","https://openalex.org/W3191089618","https://openalex.org/W3210711230","https://openalex.org/W4206078729","https://openalex.org/W4206419503","https://openalex.org/W4207012249","https://openalex.org/W4294000785","https://openalex.org/W4366991255","https://openalex.org/W4375863032","https://openalex.org/W4378782647","https://openalex.org/W4385790266","https://openalex.org/W4391449921","https://openalex.org/W4406243633"],"related_works":["https://openalex.org/W611386996","https://openalex.org/W2371343292","https://openalex.org/W629290331","https://openalex.org/W4206379684","https://openalex.org/W617685022","https://openalex.org/W1509983653","https://openalex.org/W3215563689","https://openalex.org/W610590827","https://openalex.org/W591599671","https://openalex.org/W4390443207"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identification":[1],"of":[2,11,18,39,49,87,184,222,244],"drug":[3,13],"target":[4],"interactions":[5,177],"(DTI)":[6],"is":[7,23,41,139,203],"an":[8],"important":[9],"part":[10],"the":[12,47,142,160,182,185,197,208,212,218,223,241,245],"discovery":[14],"process.":[15,115,195],"Since":[16],"prediction":[17,38,114,194,220],"DTI":[19,40,113,125,193],"using":[20,30,233],"laboratory":[21],"tests":[22],"time":[24],"consuming":[25],"and":[26,53,79,90,94,103,147,167,174,188],"laborious,":[27],"automated":[28],"tools":[29],"computational":[31,88],"intelligence":[32],"(CI)":[33],"techniques":[34],"become":[35],"essential.":[36],"The":[37,59,70,96,136],"a":[42,85,123,226],"challenging":[43],"process":[44,229],"due":[45],"to":[46,92,140,152,180,205],"absence":[48],"known":[50],"drug-target":[51],"relationship":[52],"no":[54],"experimentally":[55],"verified":[56],"negative":[57],"samples.":[58],"datasets":[60],"with":[61,133],"limited":[62],"or":[63],"unbalanced":[64],"data,":[65],"do":[66],"not":[67],"perform":[68],"well.":[69],"models":[71,107],"that":[72,118],"use":[73],"heterogeneous":[74],"networks,":[75],"non-linear":[76],"fusion":[77],"techniques,":[78],"heuristic":[80],"similarity":[81],"selection":[82],"may":[83],"need":[84],"lot":[86],"power":[89],"experience":[91],"implement":[93],"fine-tune.":[95],"latest":[97],"developments":[98],"in":[99,144,211],"machine":[100],"learning":[101,105],"(ML)":[102],"deep":[104],"(DL)":[106],"can":[108],"be":[109],"employed":[110,179,190],"for":[111,191],"effective":[112],"RESULTS:":[116],"To":[117,157],"end,":[119],"this":[120],"study":[121,239],"develops":[122],"novel":[124],"Prediction":[126,132],"model,":[127,225],"namely,":[128],"DTIP-WINDGRU":[129,162,224,246],"Drug-Target":[130],"Interaction":[131],"Wind-Enhanced":[134],"GRU.":[135],"major":[137],"aim":[138],"determine":[141],"DTIs":[143],"both":[145],"labelled":[146],"unlabelled":[148],"samples":[149],"accurately":[150],"compared":[151],"traditional":[153],"wet":[154],"lab":[155],"experiments.":[156],"accomplish":[158],"this,":[159],"proposed":[161],"model":[163,187,247],"primarily":[164],"performs":[165],"pre-processing":[166],"class":[168],"labelling.":[169],"In":[170],"addition,":[171],"drug-to-drug":[172],"(D-D)":[173],"target-to-target":[175],"(T-T)":[176],"are":[178,189],"initialize":[181],"weights":[183],"GRU":[186,213],"the,":[192],"Finally,":[196],"Wind":[198],"Driven":[199],"Optimization":[200],"(WDO)":[201],"algorithm":[202],"utilized":[204],"optimally":[206],"choose":[207],"hyperparameters":[209],"involved":[210],"model.":[214],"CONCLUSIONS:":[215],"For":[216],"ensuring":[217],"effectual":[219],"results":[221],"widespread":[227],"experimentation":[228],"was":[230],"carried":[231],"out":[232],"four":[234],"datasets.":[235],"This":[236],"comprehensive":[237],"comparative":[238],"highlighted":[240],"better":[242],"performance":[243],"over":[248],"existing":[249],"techniques.":[250]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}