{"id":"https://openalex.org/W4412030374","doi":"https://doi.org/10.1109/access.2025.3585601","title":"Deep Pseudogene Categorization and Genome-Wide Transcription Prediction Using GANP-Based Feature Selection and TabNet Interpretability","display_name":"Deep Pseudogene Categorization and Genome-Wide Transcription Prediction Using GANP-Based Feature Selection and TabNet Interpretability","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4412030374","doi":"https://doi.org/10.1109/access.2025.3585601"},"language":"en","primary_location":{"id":"doi:10.1109/access.2025.3585601","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3585601","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2025.3585601","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Zeeshan Ahmed","orcid":"https://orcid.org/0009-0005-8514-9625"},"institutions":[{"id":"https://openalex.org/I4210102737","display_name":"Khwaja Fareed University of Engineering and Information Technology","ror":"https://ror.org/0161dyt30","country_code":"PK","type":"education","lineage":["https://openalex.org/I4210102737"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Zeeshan Ahmed","raw_affiliation_strings":["Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan","Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Abu Dhabi Road, Rahim Yar Khan, Punjab, Pakistan"],"raw_orcid":"https://orcid.org/0009-0005-8514-9625","affiliations":[{"raw_affiliation_string":"Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan","institution_ids":["https://openalex.org/I4210102737"]},{"raw_affiliation_string":"Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Abu Dhabi Road, Rahim Yar Khan, Punjab, Pakistan","institution_ids":["https://openalex.org/I4210102737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039561400","display_name":"Kashif Munir","orcid":"https://orcid.org/0000-0001-5114-4213"},"institutions":[{"id":"https://openalex.org/I4210102737","display_name":"Khwaja Fareed University of Engineering and Information Technology","ror":"https://ror.org/0161dyt30","country_code":"PK","type":"education","lineage":["https://openalex.org/I4210102737"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Kashif Munir","raw_affiliation_strings":["Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan","Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Abu Dhabi Road, Rahim Yar Khan, Punjab, Pakistan"],"raw_orcid":"https://orcid.org/0000-0001-5114-4213","affiliations":[{"raw_affiliation_string":"Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan","institution_ids":["https://openalex.org/I4210102737"]},{"raw_affiliation_string":"Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Abu Dhabi Road, Rahim Yar Khan, Punjab, Pakistan","institution_ids":["https://openalex.org/I4210102737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113251686","display_name":"Muhammad Usama Tanveer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210102737","display_name":"Khwaja Fareed University of Engineering and Information Technology","ror":"https://ror.org/0161dyt30","country_code":"PK","type":"education","lineage":["https://openalex.org/I4210102737"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Usama Tanveer","raw_affiliation_strings":["Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan","Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Abu Dhabi Road, Rahim Yar Khan, Punjab, Pakistan"],"raw_orcid":"https://orcid.org/0009-0002-7374-9461","affiliations":[{"raw_affiliation_string":"Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan","institution_ids":["https://openalex.org/I4210102737"]},{"raw_affiliation_string":"Institute of Information Technology, Khwaja Fareed University of Engineering and Information Technology, Abu Dhabi Road, Rahim Yar Khan, Punjab, Pakistan","institution_ids":["https://openalex.org/I4210102737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003756558","display_name":"Syed Rizwan Hassan","orcid":"https://orcid.org/0000-0002-6206-3934"},"institutions":[{"id":"https://openalex.org/I12832649","display_name":"Gachon University","ror":"https://ror.org/03ryywt80","country_code":"KR","type":"education","lineage":["https://openalex.org/I12832649"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Syed Rizwan Hassan","raw_affiliation_strings":["Department of Computer Engineering, Gachon University, Seongnam-si, South Korea"],"raw_orcid":"https://orcid.org/0000-0002-6206-3934","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Gachon University, Seongnam-si, South Korea","institution_ids":["https://openalex.org/I12832649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037676122","display_name":"Ateeq Ur Rehman","orcid":"https://orcid.org/0000-0001-5203-0621"},"institutions":[{"id":"https://openalex.org/I85461943","display_name":"Saveetha University","ror":"https://ror.org/0034me914","country_code":"IN","type":"education","lineage":["https://openalex.org/I85461943"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Ateeq Ur Rehman","raw_affiliation_strings":["Computer Science and Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India"],"raw_orcid":"https://orcid.org/0000-0001-5203-0621","affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India","institution_ids":["https://openalex.org/I85461943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091127899","display_name":"Habib Hamam","orcid":"https://orcid.org/0000-0002-5320-1012"},"institutions":[{"id":"https://openalex.org/I154799132","display_name":"Universit\u00e9 de Moncton","ror":"https://ror.org/029tnqt29","country_code":"CA","type":"education","lineage":["https://openalex.org/I154799132"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Habib Hamam","raw_affiliation_strings":["Faculty of Engineering, Universit&#x00E9; de Moncton, Moncton, NB, Canada","Faculty of Engineering, Uni de Moncton, Moncton, NB, Canada"],"raw_orcid":"https://orcid.org/0000-0002-5320-1012","affiliations":[{"raw_affiliation_string":"Faculty of Engineering, Universit&#x00E9; de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]},{"raw_affiliation_string":"Faculty of Engineering, Uni de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210102737"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.6802,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.70695371,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"13","issue":null,"first_page":"118096","last_page":"118111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9645000100135803,"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":0.9645000100135803,"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/interpretability","display_name":"Interpretability","score":0.8149457573890686},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7668489217758179},{"id":"https://openalex.org/keywords/pseudogene","display_name":"Pseudogene","score":0.7398732900619507},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.6908579468727112},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5563576817512512},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.5170417428016663},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.49581846594810486},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4697079062461853},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.44601279497146606},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4348057806491852},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37272703647613525},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32156193256378174},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25292861461639404},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23288074135780334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20812109112739563}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8149457573890686},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7668489217758179},{"id":"https://openalex.org/C34957205","wikidata":"https://www.wikidata.org/wiki/Q277338","display_name":"Pseudogene","level":4,"score":0.7398732900619507},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.6908579468727112},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5563576817512512},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.5170417428016663},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.49581846594810486},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4697079062461853},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.44601279497146606},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4348057806491852},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37272703647613525},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32156193256378174},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25292861461639404},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23288074135780334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20812109112739563},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2025.3585601","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3585601","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:e659238bf01e45bcb7420fceb610630c","is_oa":true,"landing_page_url":"https://doaj.org/article/e659238bf01e45bcb7420fceb610630c","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":"IEEE Access, Vol 13, Pp 118096-118111 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2025.3585601","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3585601","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W964460774","https://openalex.org/W1909808974","https://openalex.org/W1941659294","https://openalex.org/W1953477380","https://openalex.org/W1974352732","https://openalex.org/W2034342958","https://openalex.org/W2046183549","https://openalex.org/W2088794999","https://openalex.org/W2111466507","https://openalex.org/W2127143129","https://openalex.org/W2144882930","https://openalex.org/W2162558393","https://openalex.org/W2180747979","https://openalex.org/W2587935651","https://openalex.org/W2768149277","https://openalex.org/W2770808765","https://openalex.org/W2800788706","https://openalex.org/W2898336531","https://openalex.org/W2949884285","https://openalex.org/W2997837308","https://openalex.org/W3102927640","https://openalex.org/W3116804779","https://openalex.org/W3174086521","https://openalex.org/W4210572383","https://openalex.org/W4226239514","https://openalex.org/W4238870146","https://openalex.org/W4256049924","https://openalex.org/W4282939265","https://openalex.org/W4307216773","https://openalex.org/W4386846548","https://openalex.org/W4396710633","https://openalex.org/W4399996736","https://openalex.org/W4408221795","https://openalex.org/W4409184613","https://openalex.org/W4409313023","https://openalex.org/W6780640948","https://openalex.org/W6878140016","https://openalex.org/W6879438976"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W1977805690","https://openalex.org/W2769050893","https://openalex.org/W2003343781","https://openalex.org/W2367624822","https://openalex.org/W4310278675","https://openalex.org/W2808331510","https://openalex.org/W4388422664","https://openalex.org/W2144270675"],"abstract_inverted_index":{"Pseudogenes,":[0],"once":[1],"regarded":[2],"as":[3,8,129],"genomic":[4,210],"relics,":[5],"have":[6],"emerged":[7],"critical":[9],"regulators":[10],"of":[11,37,119,194,205,229],"gene":[12],"expression,":[13],"influencing":[14],"cancer,":[15],"neurodegenerative":[16],"disorders,":[17],"and":[18,60,79,87,98,132,154,174,186,197,212,227,238],"developmental":[19],"processes.":[20],"This":[21,164],"study":[22],"introduces":[23],"an":[24,45,117],"advanced":[25],"framework":[26,115],"for":[27,47,56,64,157,171,236],"pseudogene":[28,172,230],"classification,":[29],"leveraging":[30],"deep":[31,195],"learning":[32,124,196],"to":[33,94,103,208],"address":[34],"the":[35,192,202],"challenges":[36],"large-scale":[38,110],"transcriptomic":[39,112],"analysis.":[40],"The":[41,90,139,189],"proposed":[42],"approach":[43],"integrates":[44],"autoencoder":[46],"dimensionality":[48],"reduction,":[49],"a":[50,61,109,167,217,233],"conditional":[51],"generative":[52,198],"adversarial":[53],"network":[54],"(cGAN)":[55],"synthetic":[57,100],"data":[58],"generation,":[59],"TabNet":[62],"classifier":[63],"final":[65],"prediction.":[66],"Extensive":[67],"literature":[68],"on":[69,108,144],"pseudogenes":[70],"highlights":[71],"their":[72],"interaction":[73],"with":[74,160,178],"coding":[75],"genes,":[76],"non-coding":[77,175],"RNAs,":[78],"epigenetic":[80],"mechanisms,":[81],"which":[82],"are":[83],"pivotal":[84],"in":[85,181,200],"transcriptional":[86],"post-transcriptional":[88],"regulation.":[89],"pipeline":[91],"uses":[92],"SMOTE":[93],"mitigate":[95],"class":[96],"imbalance":[97],"applies":[99],"feature":[101],"augmentation":[102],"boost":[104],"classification":[105],"performance.":[106],"Tested":[107],"curated":[111],"dataset,":[113],"our":[114],"achieves":[116],"accuracy":[118],"96%,":[120],"surpassing":[121],"traditional":[122],"machine":[123],"models.":[125],"Visualization":[126],"tools":[127],"such":[128],"t-SNE,":[130],"heatmaps,":[131],"SHAP":[133],"plots":[134],"further":[135],"enhance":[136],"model":[137],"interpretability.":[138],"system":[140],"is":[141],"fully":[142],"implemented":[143],"accessible":[145],"AI":[146],"platforms":[147],"(Google":[148],"Colab,":[149],"Kaggle),":[150],"ensuring":[151],"real-time":[152],"simulation":[153],"reproducibility,":[155],"especially":[156],"research":[158],"teams":[159],"limited":[161],"computational":[162],"resources.":[163],"method":[165],"offers":[166],"scalable,":[168],"explainable":[169],"solution":[170],"identification":[173],"RNA":[176],"characterization,":[177],"broad":[179],"applications":[180],"cancer":[182],"research,":[183],"genome":[184],"annotation,":[185],"precision":[187,214],"transcriptomics.":[188],"results":[190],"underscore":[191],"power":[193],"models":[199],"unveiling":[201],"regulatory":[203],"complexity":[204],"pseudogenes,":[206],"contributing":[207],"future":[209],"studies":[211],"clinical":[213],"medicine.":[215],"Additionally,":[216],"user-friendly":[218],"Gradio":[219],"interface":[220],"has":[221],"been":[222],"developed,":[223],"enabling":[224],"interactive":[225],"exploration":[226],"prediction":[228],"classes,":[231],"providing":[232],"practical":[234],"tool":[235],"biologists":[237],"clinicians":[239],"alike.":[240]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
